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NORMAL GENOMIC

• Dominguez DC, Guragain M, Patrauchan M
• Calcium binding proteins and calcium signaling in prokaryotes.
• Cell Calcium. 2015; 57: 151-65
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• With the continued increase of genomic information and computational analyses during the recent years, the number of newly discovered calcium binding proteins (CaBPs) in prokaryotic organisms has increased dramatically. These proteins contain sequences that closely resemble a variety of eukaryotic calcium (Ca(2+)) binding motifs including the canonical and pseudo EF-hand motifs, Ca(2+)-binding beta-roll, Greek key motif and a novel putative Ca(2+)-binding domain, called the Big domain. Prokaryotic CaBPs have been implicated in diverse cellular activities such as division, development, motility, homeostasis, stress response, secretion, transport, signaling and host-pathogen interactions. However, the majority of these proteins are hypothetical, and only few of them have been studied functionally. The finding of many diverse CaBPs in prokaryotic genomes opens an exciting area of research to explore and define the role of Ca(2+) in organisms other than eukaryotes. This review presents the most recent developments in the field of CaBPs and novel advancements in the role of Ca(2+) in prokaryotes.

• Syed K, Mashele SS
• Comparative analysis of P450 signature motifs EXXR and CXG in the large and diverse kingdom of fungi: identification of evolutionarily conserved amino acid patterns characteristic of P450 family.
• PLoS One. 2014; 9: 95616-95616
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• Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins distributed across the biological kingdoms. P450s are catalytically versatile and play key roles in organisms primary and secondary metabolism. Identification of P450s across the biological kingdoms depends largely on the identification of two P450 signature motifs, EXXR and CXG, in the protein sequence. Once a putative protein has been identified as P450, it will be assigned to a family and subfamily based on the criteria that P450s within a family share more than 40% homology and members of subfamilies share more than 55% homology. However, to date, no evidence has been presented that can distinguish members of a P450 family. Here, for the first time we report the identification of EXXR- and CXG-motifs-based amino acid patterns that are characteristic of the P450 family. Analysis of P450 signature motifs in the under-explored fungal P450s from four different phyla, ascomycota, basidiomycota, zygomycota and chytridiomycota, indicated that the EXXR motif is highly variable and the CXG motif is somewhat variable. The amino acids threonine and leucine are preferred as second and third amino acids in the EXXR motif and proline and glycine are preferred as second and third amino acids in the CXG motif in fungal P450s. Analysis of 67 P450 families from biological kingdoms such as plants, animals, bacteria and fungi showed conservation of a set of amino acid patterns characteristic of a particular P450 family in EXXR and CXG motifs. This suggests that during the divergence of P450 families from a common ancestor these amino acids patterns evolve and are retained in each P450 family as a signature of that family. The role of amino acid patterns characteristic of a P450 family in the structural and/or functional aspects of members of the P450 family is a topic for future research.

• Mazumder M, Padhan N, Bhattacharya A, Gourinath S
• Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca(2)(+) binding affinity.
• PLoS One. 2014; 9: 96202-96202
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• The diversity of functions carried out by EF hand-containing calcium-binding proteins is due to various interactions made by these proteins as well as the range of affinity levels for Ca(2)(+) displayed by them. However, accurate methods are not available for prediction of binding affinities. Here, amino acid patterns of canonical EF hand sequences obtained from available crystal structures were used to develop a classifier that distinguishes Ca(2)(+)-binding loops and non Ca(2)(+)-binding regions with 100% accuracy. To investigate further, we performed a proteome-wide prediction for E. histolytica, and classified known EF-hand proteins. We compared our results with published methods on the E. histolytica proteome scan, and demonstrated our method to be more specific and accurate for predicting potential canonical Ca(2)(+)-binding loops. Furthermore, we annotated canonical EF-hand motifs and classified them based on their Ca(2)(+)-binding affinities using support vector machines. Using a novel method generated from position-specific scoring metrics and then tested against three different experimentally derived EF-hand-motif datasets, predictions of Ca(2)(+)-binding affinities were between 87 and 90% accurate. Our results show that the tool described here is capable of predicting Ca(2)(+)-binding affinity constants of EF-hand proteins.

• Kawasaki H, Kretsinger RH
• Structural differences among subfamilies of EF-hand proteins--a view from the pseudo two-fold symmetry axis.
• Proteins. 2014; 82: 2915-24
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• We have analyzed the conformations of EF-lobes, adjacent pairs of EF-hand domains, in a coordinate system based on the approximate two-fold (z) axis that relates the two EF-hands. Two parameters - dE(o), the azimuthal angle between the y-axis and the projection of the offset vector to helix E onto the yz-plane, and deltadF(o), the difference angle between the two helices (F1 and F2) of odd and even domains--characterize the openness of a single EF-hand domain and of an EF-lobe, respectively. We describe and compare values of dE(o) and of deltadF(o) for EF-hand proteins of five subfamilies--CTER, CPV, S100, PARV, CALP--in calci- and apo- forms, with and without bound target proteins. Each subfamily has characteristic changes associated with binding calcium and/or target proteins.

• Sadeghi L, Khajeh K, Mollania N, Dabirmanesh B, Ranjbar B
• Extra EF hand unit (DX) mediated stabilization and calcium independency of alpha-amylase.
• Mol Biotechnol. 2013; 53: 270-7
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• It is the common feature of alpha-amylases that calcium ion is required for their structural integrity and thermal stability. All amylases have at least one Ca(2+) per molecule; therefore amino acids involved in calcium binding are specific and conserved. In this study, sequence analysis revealed the presence of EF-hand-like motif in calcium-binding loop of Bacillus megaterium WHO (BMW)-amylase that was previously isolated from BMW. The EF-hand motif and its variants (EF-hand-like motif) are the most common calcium-binding motifs found in a large number of protein families. To investigate the effect of calcium ion on the thermal stability and activity of BMW-amylase, we used site-directed mutagenesis to replace histidine 58 with Asp (D), Ile (I), Tyr (Y), Phe (F), and Arg (R) at the seventh position of EF-hand-like motif. Upon the addition of an extra DX unit to the calcium-binding loop in H58D variant, thermal stability, catalytic activity, and chelating power of the enzyme improved due to higher affinity toward calcium. H58D variant demonstrated calcium independency compared to the wild type and other created mutants. Conformational changes in the presence and absence of Ca(2+) were monitored using fluorescence technique.

• Osuna J, Flores H, Gaytan P
• A reporter system that discriminates EF-hand-sensor motifs from signal-modulators at the single-motif level.
• FEBS Lett. 2012; 586: 3398-403
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• The T-protein is a single-polypeptide bi-functional enzyme composed of a chorismate mutase domain fused to a prephenate dehydrogenase domain (TyrA). We replaced the chorismate mutase domain with canonical or pseudo-Ca(2+)-binding motifs (EF-hand). Canonical-EF-hand-motifs differentiate from pseudo-EF-hand-motifs by experimenting a Ca(2+)-dependent conformational change. The Ca(2+)-free EF-hand-TyrA fusion-proteins showed TyrA activity at the T-protein level. Canonical-EF-hand-TyrA fusions showed a Ca(2+)-dependent loss of TyrA activity, but a pseudo-EF-hand-TyrA fusion showed high TyrA activity level in excess-Ca(2+) conditions. Because TyrA activity exhibits robust changes in response to Ca(2+)-dependent-EF-hand conformational alterations, TyrA could be a good Ca(2+)-reporter enzyme. A chimeric canonical/pseudo-EF-hand strategy is proposed to confer pseudo-EF-hand motifs with a Ca(2+)-dependent conformational change.

• Di Sole F, Vadnagara K, Moe OW, Babich V
• Calcineurin homologous protein: a multifunctional Ca2+-binding protein family.
• Am J Physiol Renal Physiol. 2012; 303: 16579-16579
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• The calcineurin homologous protein (CHP) belongs to an evolutionarily conserved Ca(2+)-binding protein subfamily. The CHP subfamily is composed of CHP1, CHP2, and CHP3, which in vertebrates share significant homology at the protein level with each other and between other Ca(2+)-binding proteins. The CHP structure consists of two globular domains containing from one to four EF-hand structural motifs (calcium-binding regions composed of two helixes, E and F, joined by a loop), the myristoylation, and nuclear export signals. These structural features are essential for the function of the three members of the CHP subfamily. Indeed, CHP1-CHP3 have multiple and diverse essential functions, ranging from the regulation of the plasma membrane Na(+)/H(+) exchanger protein function, to carrier vesicle trafficking and gene transcription. The diverse functions attributed to the CHP subfamily rendered an understanding of its action highly complex and often controversial. This review provides a comprehensive and organized examination of the properties and physiological roles of the CHP subfamily with a view to revealing a link between CHP diverse functions.

• Zhang Y, He CY
• Centrins in unicellular organisms: functional diversity and specialization.
• Protoplasma. 2012; 249: 459-67
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• Centrins (also known as caltractins) are conserved, EF hand-containing proteins ubiquitously found in eukaryotes. Similar to calmodulins, the calcium-binding EF hands in centrins fold into two structurally similar domains separated by an alpha-helical linker region, shaping like a dumbbell. The small size (15-22 kDa) and domain organization of centrins and their functional diversity/specialization make them an ideal system to study protein structure-function relationship. Here, we review the work on centrins with a focus on their structures and functions characterized in unicellular organisms.

• Yanez M, Gil-Longo J, Campos-Toimil M
• Calcium binding proteins.
• Adv Exp Med Biol. 2012; 740: 461-82
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• The role of Ca(2+) as a key and pivotal second messenger in cells depends largely on a wide number of heterogeneous so-called calcium binding proteins (CBP), which have the ability to bind this ion in specific domains. CBP contribute to the control of Ca(2+) concentration in the cytosol and participate in numerous cellular functions by acting as Ca(2+) transporters across cell membranes or as Ca(2+)-modulated sensors, i.e., decoding Ca(2+) signals. In this chapter we review the main Ca(2+)-modulated CBP, starting with those intracellular CBP that contain the structural EF-hand domain: parvalbumin, calmodulin, S100 proteins and calcineurin. Then, we address intracellular CBP lacking the EF-hand domain: CBP within intracellular Ca(2+) stores (paying special attention to calreticulin and calsequestrin), annexins and proteins that contain a C2 domain, such as protein kinase C (PKC) or sinaptotagmin. Finally, extracellular CBP have been classified in six groups, according to their Ca(2+) binding structures: (i) EF-hand domains; (ii) EGF-like domains; (iii) gamma-carboxyl glutamic acid (GLA)-rich domains; (iv) cadherin domains; (v) Ca(2+)-dependent (C)-type lectin-like domains; (vi) Ca(2+)-binding pockets of family C G-protein-coupled receptors. For all proteins, we briefly review their structure, location and function and additionally their potential as pharmacological targets in several human diseases.

• Orr R et al.
• FhCaBP4: a Fasciola hepatica calcium-binding protein with EF-hand and dynein light chain domains.
• Parasitol Res. 2012; 111: 1707-13
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• In trematodes, there is a family of proteins which combine EF-hand-containing domains with dynein light chain (DLC)-like domains. A member of this family from the liver fluke, Fasciola hepatica-FhCaBP4-has been identified and characterised biochemically. FhCaBP4 has an N-terminal domain containing two imperfect EF-hand sequences and a C-terminal dynein light chain-like domain. Molecular modelling predicted that the two domains are joined by a flexible linker. Native gel electrophoresis demonstrated that FhCaBP4 binds to calcium, manganese, barium and strontium ions, but not to magnesium or zinc ions. The hydrophobic, fluorescent probe 8-anilinonaphthalene-1-sulphonate bound more tightly to FhCaBP4 in the presence of calcium ions. This suggests that the protein undergoes a conformational change on ion binding which increases the number of non-polar residues on the surface. FhCaBP4 was protected from limited proteolysis by the calmodulin antagonist W7, but not by trifluoperazine or praziquantel. Protein-protein cross-linking experiments showed that FhCaBP4 underwent calcium ion-dependent dimerisation. Since DLCs are commonly dimeric, it is likely that FhCaBP4 dimerises through this domain. The molecular model reveals that the calcium ion-binding site is located close to a key sequence in the DLC-like domain, suggesting a plausible mechanism for calcium-dependent dimerisation.

• Hagen S, Brachs S, Kroczek C, Furnrohr BG, Lang C, Mielenz D
• The B cell receptor-induced calcium flux involves a calcium mediated positive feedback loop.
• Cell Calcium. 2012; 51: 411-7
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• The B cell receptor (BCR)-elicited calcium flux results in activation of mature B cells. We have recently shown that the adaptor protein Swiprosin-1/EFhd2 (EFhd2) amplifies the BCR-induced calcium flux in B cell lines. EFhd2 is a calcium binding adaptor protein with two predicted EF-hands. Here we asked whether these domains are functional and control its function. Using a blot-overlay assay with radioactive calcium we show that both EF-hands of EFhd2 have an intrinsic capacity to bind calcium. Equilibrium centrifugation confirmed that EFhd2 binds 2 calcium ions, with an apparent Kd of 110 muM. Point mutations revealed that the conserved residues E116 and E152, which reside in the canonical calcium binding loop in EF-hands 1 and 2, are essential for calcium binding by EFhd2. These mutations as well as deletion of the EF-hands, in particular EF-hand 1, abolished the ability of EFhd2 to restore BCR-induced calcium signaling in EFhd2-deficient WEHI231 cells. N-terminal deletions, but not C-terminal deletions, acted similarly. Thus, the N-terminal part of EFhd2 as well as calcium binding to its EF-hands control the intracellular calcium concentration in response to BCR stimulation in WEHI231 cells. Hence, EFhd2 regulates the BCR-elicited calcium flux through a calcium-dependent positive feedback mechanism in WEHI231 cells.

• Yanyi C, Shenghui X, Yubin Z, Jie YJ
• Calciomics: prediction and analysis of EF-hand calcium binding proteins by protein engineering.
• Sci China Chem. 2010; 53: 52-60
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• Ca(2+) plays a pivotal role in the physiology and biochemistry of prokaryotic and mammalian organisms. Viruses also utilize the universal Ca(2+) signal to create a specific cellular environment to achieve coexistence with the host, and to propagate. In this paper we first describe our development of a grafting approach to understand site-specific Ca(2+) binding properties of EF-hand proteins with a helix-loop-helix Ca(2+) binding motif, then summarize our prediction and identification of EF-hand Ca(2+) binding sites on a genome-wide scale in bacteria and virus, and next report the application of the grafting approach to probe the metal binding capability of predicted EF-hand motifs within the streptococcal hemoprotein receptor (Shr) of Streptococcus pyrogenes and the nonstructural protein 1 (nsP1) of Sindbis virus. When methods such as the grafting approach are developed in conjunction with prediction algorithms we are better able to probe continuous Ca(2+)-binding sites that have been previously underrepresented due to the limitation of conventional methodology.

• Zhao X, Pang H, Wang S, Zhou W, Yang K, Bartlam M
• Structural basis for prokaryotic calcium-mediated regulation by a Streptomyces coelicolor calcium binding protein.
• Protein Cell. 2010; 1: 771-9
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• The important and diverse regulatory roles of Ca(2+) in eukaryotes are conveyed by the EF-hand containing calmodulin superfamily. However, the calcium-regulatory proteins in prokaryotes are still poorly understood. In this study, we report the three-dimensional structure of the calcium-binding protein from Streptomyces coelicolor, named CabD, which shares low sequence homology with other known helix-loop-helix EF-hand proteins. The CabD structure should provide insights into the biological role of the prokaryotic calcium-binding proteins. The unusual structural features of CabD compared with prokaryotic EF-hand proteins and eukaryotic sarcoplasmic calcium-binding proteins, including the bending conformation of the first C-terminal alpha-helix, unpaired ligand-binding EF-hands and the lack of the extreme C-terminal loop region, suggest it may have a distinct and significant function in calcium-mediated bacterial physiological processes, and provide a structural basis for potential calcium-mediated regulatory roles in prokaryotes.

• Crow A et al.
• Crystal structure and biophysical properties of Bacillus subtilis BdbD. An oxidizing thiol:disulfide oxidoreductase containing a novel metal site.
• J Biol Chem. 2009; 284: 23719-33
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• BdbD is a thiol:disulfide oxidoreductase (TDOR) from Bacillus subtilis that functions to introduce disulfide bonds in substrate proteins/peptides on the outside of the cytoplasmic membrane and, as such, plays a key role in disulfide bond management. Here we demonstrate that the protein is membrane-associated in B. subtilis and present the crystal structure of the soluble part of the protein lacking its membrane anchor. This reveals that BdbD is similar in structure to Escherichia coli DsbA, with a thioredoxin-like domain with an inserted helical domain. A major difference, however, is the presence in BdbD of a metal site, fully occupied by Ca(2+), at an inter-domain position some 14 A away from the CXXC active site. The midpoint reduction potential of soluble BdbD was determined as -75 mV versus normal hydrogen electrode, and the active site N-terminal cysteine thiol was shown to have a low pK(a), consistent with BdbD being an oxidizing TDOR. Equilibrium unfolding studies revealed that the oxidizing power of the protein is based on the instability introduced by the disulfide bond in the oxidized form. The crystal structure of Ca(2+)-depleted BdbD showed that the protein remained folded, with only minor conformational changes. However, the reduced form of Ca(2+)-depleted BdbD was significantly less stable than reduced Ca(2+)-containing protein, and the midpoint reduction potential was shifted by approximately -20 mV, suggesting that Ca(2+) functions to boost the oxidizing power of the protein. Finally, we demonstrate that electron exchange does not occur between BdbD and B. subtilis ResA, a low potential extra-cytoplasmic TDOR.

• Ren X, Wang S, Wen Y, Yang K
• [An update of calcium signaling in bacteria--a review].
• Wei Sheng Wu Xue Bao. 2009; 49: 1564-70
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• In eukaryotes, Ca2+ is an important second messenger and regulates diverse cellular activities ranging from muscle contraction to fertilization. In bacteria, growing evidence suggests that Ca2+ also plays important regulatory roles in various physiological processes. Here we review current understanding of calcium regulation in bacteria from the following aspects: 1) the concept of bacterial [Ca2+]i and its determination; 2) cellular processes affected by [Ca2+]i changes; 3) transportation of Ca2+ across bacterial membrane; 4)eukaryotic calcium binding proteins in bacteria and their functions.

• Schwaller B
• The continuing disappearance of "pure" Ca2+ buffers.
• Cell Mol Life Sci. 2009; 66: 275-300
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• Advances in the understanding of a class of Ca(2+)-binding proteins usually referred to as "Ca(2+) buffers" are reported. Proteins historically embraced within this group include parvalbumins (alpha and beta), calbindin-D9k, calbindin-D28k and calretinin. Within the last few years a wealth of data has accumulated that allow a better understanding of the functions of particular family members of the >240 identified EF-hand Ca(2+)-binding proteins encoded by the human genome. Studies often involving transgenic animal models have revealed that they exert their specific functions within an intricate network consisting of many proteins and cellular mechanisms involved in Ca(2+) signaling and Ca(2+) homeostasis, and are thus an essential part of the Ca(2+) homeostasome. Recent results indicate that calbindin-D28k, possibly also calretinin and oncomodulin, the mammalian beta parvalbumin, might have additional Ca(2+) sensor functions, leaving parvalbumin and calbindin-D9k as the only "pure" Ca(2+) buffers.

• Mohan PM, Mukherjee S, Chary KV
• Differential native state ruggedness of the two Ca2+-binding domains in a Ca2+ sensor protein.
• Proteins. 2008; 70: 1147-53
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• Characterization of near-native excited states of a protein provides insights into various biological functions such as co-operativity, protein-ligand, and protein-protein interactions. In the present study, we investigated the ruggedness of the native state of EhCaBP using nonlinear temperature dependence of backbone amide-proton chemical shifts. EhCaBP is a two-domain EF-hand calcium sensor protein consisting of two EF-hands in each domain and binds four Ca2+ ions. It has been observed that approximately 30% of the residues in the protein access alternative conformations. Theoretical modeling suggested that these low-energy excited states are within 2-3 kcal/mol from the native state. Further, it is interesting to note that the residues accessing alternative conformations are more dominated in the C-terminal domain compared with its N-terminal counterpart suggesting that the former is more rugged in its native state. These distinct characteristics of N- and C-terminal domains of a calcium sensor protein belonging to the super family of calmodulin would have implications for domain dependent Ca2+ signaling pathways.

• Aravind P, Chandra K, Reddy PP, Jeromin A, Chary KV, Sharma Y
• Regulatory and structural EF-hand motifs of neuronal calcium sensor-1: Mg 2+ modulates Ca 2+ binding, Ca 2+ -induced conformational changes, and equilibrium unfolding transitions.
• J Mol Biol. 2008; 376: 1100-15
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• Neuronal calcium sensor-1 (NCS-1) is a major modulator of Ca(2+) signaling with a known role in neurotransmitter release. NCS-1 has one cryptic (EF1) and three functional (EF2, EF3, and EF4) EF-hand motifs. However, it is not known which are the regulatory (Ca(2+)-specific) and structural (Ca(2+)- or Mg(2+)-binding) EF-hand motifs. To understand the specialized functions of NCS-1, identification of the ionic discrimination of the EF-hand sites is important. In this work, we determined the specificity of Ca(2+) binding using NMR and EF-hand mutants. Ca(2+) titration, as monitored by [(15)N,(1)H] heteronuclear single quantum coherence, suggests that Ca(2+) binds to the EF2 and EF3 almost simultaneously, followed by EF4. Our NMR data suggest that Mg(2+) binds to EF2 and EF3, thereby classifying them as structural sites, whereas EF4 is a Ca(2+)-specific or regulatory site. This was further corroborated using an EF2/EF3-disabled mutant, which binds only Ca(2+) and not Mg(2+). Ca(2+) binding induces conformational rearrangements in the protein by reversing Mg(2+)-induced changes in Trp fluorescence and surface hydrophobicity. In a larger physiological perspective, exchanging or replacing Mg(2+) with Ca(2+) reduces the Ca(2+)-binding affinity of NCS-1 from 90 nM to 440 nM, which would be advantageous to the molecule by facilitating reversibility to the Ca(2+)-free state. Although the equilibrium unfolding transitions of apo-NCS-1 and Mg(2+)-bound NCS-1 are similar, the early unfolding transitions of Ca(2+)-bound NCS-1 are partially influenced in the presence of Mg(2+). This study demonstrates the importance of Mg(2+) as a modulator of calcium homeostasis and active-state behavior of NCS-1.

• Yamniuk AP, Gifford JL, Linse S, Vogel HJ
• Effects of metal-binding loop mutations on ligand binding to calcium- and integrin-binding protein 1. Evolution of the EF-hand?
• Biochemistry. 2008; 47: 1696-707
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• Calcium- and integrin-binding protein 1 (CIB1) is a ubiquitous, multifunctional regulatory protein consisting of four helix-loop-helix EF-hand motifs. Neither EF-I nor EF-II binds divalent metal ions; however, EF-III is a mixed Mg2+/Ca2+-binding site, and EF-IV is a higher-affinity Ca2+-specific site. Through the generation of several CIB1 mutant proteins, we have investigated the importance of the last (-Z) metal-coordinating position of EF-III (D127) and EF-IV (E172) with respect to the binding of CIB1 to Mg2+, Ca2+, and its biological target, the cytoplasmic domain of the platelet alphaIIb integrin. A D127N mutant had reduced Mg2+ and Ca2+ affinity at EF-III but retained affinity for the alphaIIb domain. A D127E mutant had increased Mg2+ and Ca2+ affinity at EF-III, but unexpectedly, the affinity for the alphaIIb domain was too low for binding to be observed. E172Q and E172D mutants showed no and weak Mg2+ binding at EF-IV, respectively, and each mutant had reduced Ca2+ affinity at EF-IV and showed moderate metal-dependent differences in affinity for the alphaIIb domain. Finally, a D127Q mutant bound Mg2+ and Ca2+ in a manner similar to that of D127N, but like that of D127E, the affinity for the alphaIIb domain was reduced below the detection limit. These data, combined with a NMR-based structural comparison of the Mg2+- and Ca2+-loaded CIB1-alphaIIb peptide complexes, suggest that the D127E and D127Q mutations have a disruptive effect on alphaIIb binding since they expand the metal-binding loop and change the alpha-helix positions in EF-III. Conversely, upon replacement of the ancestral Glu with Asp at the -Z position of EF-III, CIB1 gained affinity for alphaIIb, and the Ca2+ affinity of CIB1 shifted into a range where the protein is able to act as an intracellular Ca2+ sensor.

• Murai MJ et al.
• Characterization of the C-terminal half of human juvenile myoclonic epilepsy protein EFHC1: dimer formation blocks Ca2+ and Mg2+ binding to its functional EF-hand.
• Arch Biochem Biophys. 2008; 477: 131-8
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• Human EFHC1 is a member of the EF-hand superfamily of Ca(2+)-binding proteins with three DM10 domains of unclear function. Point mutations in the EFHC1 gene are related to juvenile myoclonic epilepsy, a fairly common idiopathic generalized epilepsy. Here, we report the first structural and thermodynamic analyses of the EFHC1C-terminus (residues 403-640; named EFHC1C), comprising the last DM10 domain and the EF-hand motif. Circular dichroism spectroscopy revealed that the secondary structure of EFHC1C is composed by 34% of alpha-helices and 17% of beta-strands. Size exclusion chromatography and mass spectrometry showed that under oxidizing condition EFHC1C dimerizes through the formation of disulfide bond. Tandem mass spectrometry (MS/MS) analysis of peptides generated by trypsin digestion suggests that the Cys575 is involved in intermolecular S-S bond. In addition, DTNB assay showed that each reduced EFHC1C molecule has one accessible free thiol. Isothermal titration calorimetry (ITC) showed that while the interaction between Ca(2+) and EFHC1C is enthalpically driven (DeltaH=-58.6 to -67 kJ/mol and TDeltaS=-22.5 to -31 kJ/mol) the interaction between Mg(2+) and EFHC1C involves an entropic gain, and is approximately 5 times less enthalpically favorable (DeltaH=-11.7 to -14 kJ/mol and TDeltaS=21.9 to 19 kJ/mol) than for Ca(2+) binding. It was also found that under reducing condition Ca(2+) or Mg(2+) ions bind to EFHC1C in a 1/1 molar ratio, while under oxidizing condition this ratio is reduced, showing that EFHC1C dimerization blocks Ca(2+) and Mg(2+) binding.

• Olah Z et al.
• Anti-calmodulins and tricyclic adjuvants in pain therapy block the TRPV1 channel.
• PLoS One. 2007; 2: 545-545
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• Ca(2+)-loaded calmodulin normally inhibits multiple Ca(2+)-channels upon dangerous elevation of intracellular Ca(2+) and protects cells from Ca(2+)-cytotoxicity, so blocking of calmodulin should theoretically lead to uncontrolled elevation of intracellular Ca(2+). Paradoxically, classical anti-psychotic, anti-calmodulin drugs were noted here to inhibit Ca(2+)-uptake via the vanilloid inducible Ca(2+)-channel/inflamatory pain receptor 1 (TRPV1), which suggests that calmodulin inhibitors may block pore formation and Ca(2+) entry. Functional assays on TRPV1 expressing cells support direct, dose-dependent inhibition of vanilloid-induced (45)Ca(2+)-uptake at microM concentrations: calmidazolium (broad range) > or = trifluoperazine (narrow range) chlorpromazine/amitriptyline>fluphenazine>>W-7 and W-13 (only partially). Most likely a short acidic domain at the pore loop of the channel orifice functions as binding site either for Ca(2+) or anti-calmodulin drugs. Camstatin, a selective peptide blocker of calmodulin, inhibits vanilloid-induced Ca(2+)-uptake in intact TRPV1(+) cells, and suggests an extracellular site of inhibition. TRPV1(+), inflammatory pain-conferring nociceptive neurons from sensory ganglia, were blocked by various anti-psychotic and anti-calmodulin drugs. Among them, calmidazolium, the most effective calmodulin agonist, blocked Ca(2+)-entry by a non-competitive kinetics, affecting the TRPV1 at a different site than the vanilloid binding pocket. Data suggest that various calmodulin antagonists dock to an extracellular site, not found in other Ca(2+)-channels. Calmodulin antagonist-evoked inhibition of TRPV1 and NMDA receptors/Ca(2+)-channels was validated by microiontophoresis of calmidazolium to laminectomised rat monitored with extracellular single unit recordings in vivo. These unexpected findings may explain empirically noted efficacy of clinical pain adjuvant therapy that justify efforts to develop hits into painkillers, selective to sensory Ca(2+)-channels but not affecting motoneurons.

• Jobby MK, Sharma Y
• Caulollins from Caulobacter crescentus, a pair of partially unstructured proteins of betagamma-crystallin superfamily, gain structure upon binding calcium.
• Biochemistry. 2007; 46: 12298-307
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• The betagamma-crystallin superfamily comprises members from various taxa and species, which have similar domain topologies as that of lens beta- and gamma-crystallins. We have studied new microbial members of this understudied betagamma-crystallin superfamily from the bacterium Caulobacter crescentus. These proteins, which we named "caulollins", are paralogues with a single betagamma-crystallin domain, made up of two Greek key motifs with AB-type arrangement seen in gamma-crystallin. The second Greek key motif has Cys in place of a generally conserved Phe/Tyr residue, and the Tyr corner, considered important for the proper betagamma-crystallin fold, is missing, making this a sequentially diverse atypical betagamma-crystallin domain. This atypical domain binds two Ca2+ with moderate affinity (0.8-20 microM). In apo form, caulollins are partially unstructured proteins and gain structure upon binding Ca2+. Unlike many other microbial betagamma-crystallin domains, this domain is monomeric, though in the presence of Ca2+ it becomes more compact. Ca2+ binding increases the intrinsic stability of proteins, suggesting the role of Ca2+ as an extrinsic stabilizer. N-Terminal extension does not play any role in modulating Ca2+ binding, intrinsic stability, or oligomerization. We noted that there are several such variant domains in the genomes of unrelated species. It appears that caulollins along with these members form a subfamily in the betagamma-crystallin superfamily that would be partially unstructured in apo form, unlike many other domains from lens or microbial crystallins. This work further suggests that Ca2+ binding is a widespread feature of the betagamma-crystallin superfamily.

• Colotti G et al.
• The W105G and W99G sorcin mutants demonstrate the role of the D helix in the Ca(2+)-dependent interaction with annexin VII and the cardiac ryanodine receptor.
• Biochemistry. 2006; 45: 12519-29
• Display abstract

• Sorcin, a 21.6 kDa two-domain penta-EF-hand (PEF) protein, when activated by Ca(2+) binding, interacts with target proteins in a largely uncharacterized process. The two physiological EF-hands EF3 and EF2 do not belong to a structural pair but are connected by the D helix. To establish whether this helix is instrumental in sorcin activation, two D helix residues were mutated: W105, located near EF3 and involved in a network of interactions, and W99, located near EF2 and facing solvent, were substituted with glycine. Neither mutation alters calcium affinity. The interaction of the W105G and W99G mutants with annexin VII and the cardiac ryanodine receptor (RyR2), requiring the sorcin N-terminal and C-terminal domain, respectively, was studied. Surface plasmon resonance experiments show that binding of annexin VII to W99G occurs at the same Ca(2+) concentration as that of the wild type, whereas W105G requires a significantly higher Ca(2+) concentration. Ca(2+) spark activity of isolated heart cells monitors the sorcin-RyR2 interaction and is unaltered by W105G but is reduced equally by W99G and the wild type. Thus, substitution of W105, via disruption of the network of D helix interactions, affects the capacity of sorcin to recognize and interact with either target at physiological Ca(2+) concentrations, while mutation of solvent-facing W99 has little effect. The D helix appears to amplify the localized structural changes that occur at EF3 upon Ca(2+) binding and thereby trigger a structural rearrangement that enables interaction of sorcin with its molecular targets. The same activation process may apply to other PEF proteins in view of the D helix conservation.

• Spratt DE, Newman E, Mosher J, Ghosh DK, Salerno JC, Guillemette JG
• Binding and activation of nitric oxide synthase isozymes by calmodulin EF hand pairs.
• FEBS J. 2006; 273: 1759-71
• Display abstract

• Calmodulin (CaM) is a cytosolic Ca(2+) signal-transducing protein that binds and activates many different cellular enzymes with physiological relevance, including the nitric oxide synthase (NOS) isozymes. CaM consists of two globular domains joined by a central linker; each domain contains an EF hand pair. Four different mutant CaM proteins were used to investigate the role of the two CaM EF hand pairs in the binding and activation of the mammalian inducible NOS (iNOS) and the constitutive NOS (cNOS) enzymes, endothelial NOS (eNOS) and neuronal NOS (nNOS). The role of the CaM EF hand pairs in different aspects of NOS enzymatic function was monitored using three assays that monitor electron transfer within a NOS homodimer. Gel filtration studies were used to determine the effect of Ca(2+) on the dimerization of iNOS when coexpressed with CaM and the mutant CaM proteins. Gel mobility shift assays were performed to determine binding stoichiometries of CaM proteins to synthetic NOS CaM-binding domain peptides. Our results show that the N-terminal EF hand pair of CaM contains important binding and activating elements for iNOS, whereas the N-terminal EF hand pair in conjunction with the central linker region is required for cNOS enzyme binding and activation. The iNOS enzyme must be coexpressed with wild-type CaM in vitro because of its propensity to aggregate when residues of the highly hydrophobic CaM-binding domain are exposed to an aqueous environment. A possible role for iNOS aggregation in vivo is also discussed.

• Zhou Y, Yang W, Kirberger M, Lee HW, Ayalasomayajula G, Yang JJ
• Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins.
• Proteins. 2006; 65: 643-55
• Display abstract

• The EF-hand protein with a helix-loop-helix Ca(2+) binding motif constitutes one of the largest protein families and is involved in numerous biological processes. To facilitate the understanding of the role of Ca(2+) in biological systems using genomic information, we report, herein, our improvement on the pattern search method for the identification of EF-hand and EF-like Ca(2+)-binding proteins. The canonical EF-hand patterns are modified to cater to different flanking structural elements. In addition, on the basis of the conserved sequence of both the N- and C-terminal EF-hands within S100 and S100-like proteins, a new signature profile has been established to allow for the identification of pseudo EF-hand and S100 proteins from genomic information. The new patterns have a positive predictive value of 99% and a sensitivity of 96% for pseudo EF-hands. Furthermore, using the developed patterns, we have identified zero pseudo EF-hand motif and 467 canonical EF-hand Ca(2+) binding motifs with diverse cellular functions in the bacteria genome. The prediction results imply that pseudo EF-hand motifs are phylogenetically younger than canonical EF-hand motifs. Our prediction of Ca(2+) binding motifs provides not only an insight into the role of Ca(2+) and Ca(2+)-binding proteins in bacterial systems, but also a way to explore and define the role of Ca(2+) in other biological systems (calciomics).

• Capozzi F, Casadei F, Luchinat C
• EF-hand protein dynamics and evolution of calcium signal transduction: an NMR view.
• J Biol Inorg Chem. 2006; 11: 949-62
• Display abstract

• Calcium signaling, one of the most widespread signaling mechanisms in cells, is generally carried out by EF-hand proteins, characterized by a helix-loop-helix motif paired in functional domains. EF-hand proteins may be viewed as molecular switches activated by calcium concentration transients. The EF-hand structural database has grown to a point where meaningful inferences on the functional conformational rearrangements upon calcium binding can be made by comparing a fair number of pairs of end points, i.e., the structures of the apo and calcium-bound forms. More compact descriptors of the movement associated with calcium binding, in terms of principal component analysis of the six interhelical angles, have also become available. Dynamic information obtained by NMR, also with the aid of calcium substitution with paramagnetic lanthanides, is shedding light on the intrinsic amplitude of the conformational degrees of freedom sampled by the various members of the EF-hand superfamily, as well as on the time scales of the motions. Particularly, NMR of lanthanide derivatives helps in capturing long time scale motions. Both static and dynamic pictures reveal a large variety of behaviors. It is increasingly recognized that the EF-hand machinery has differentiated its behavior during evolution in several ways, e.g., by modifying one of the loops, by undergoing a further duplication after the initial motif duplication that originated the functional domain, or by acquiring the ability to dimerize.

• Muralidhar D, Kunjachen Jobby M, Jeromin A, Roder J, Thomas F, Sharma Y
• Calcium and chlorpromazine binding to the EF-hand peptides of neuronal calcium sensor-1.
• Peptides. 2004; 25: 909-17
• Display abstract

• Neuronal calcium sensor-1, a protein of calcium sensor family, is known to have four structural EF-hands. We have synthesised peptides corresponding to all the four EF-hands and studied their conformation and calcium-binding. Our data confirm that the first putative site, a non-canonical one (EF1), does not bind calcium. We have investigated if this lack of binding is due to the presence of non-favoured residues (particularly at +x and -z co-ordinating positions) of the loop. We have mutated these residues and found that after modification the peptides bound calcium. However, these mutated peptides (EF1 and its functional mutants) do not show any Ca(2+) induced changes in far-UV CD. EF2, EF3, and EF4 peptides bind Ca(2+), EF3 being the strongest binder, followed by EF4. Our data of Ca(2+)-binding to individual EF peptides show that there are three active Ca(2+)-binding sites in NCS-1. We have also studied the binding of a neuroleptic drug, chlorpromazine, with the protein as well as with its EF-hands. CPZ binds myristoylated as well as non-myristoylated NCS-1 in Ca(2+)-dependent manner, with dynamic interaction to myristoylated protein. CPZ does not bind to EF1, but binds to functional EF-hand peptides and induces changes in far-UV CD. Our results suggest that NCS-1 could be a target of such antipsychotic and neuroleptic drugs.

• Dai H, Shin OH, Machius M, Tomchick DR, Sudhof TC, Rizo J
• Structural basis for the evolutionary inactivation of Ca2+ binding to synaptotagmin 4.
• Nat Struct Mol Biol. 2004; 11: 844-9
• Display abstract

• The neuronal protein synaptotagmin 1 functions as a Ca(2+) sensor in exocytosis via two Ca(2+)-binding C(2) domains. The very similar synaptotagmin 4, which includes all the predicted Ca(2+)-binding residues in the C(2)B domain but not in the C(2)A domain, is also thought to function as a neuronal Ca(2+) sensor. Here we show that, unexpectedly, both C(2) domains of fly synaptotagmin 4 exhibit Ca(2+)-dependent phospholipid binding, whereas neither C(2) domain of rat synaptotagmin 4 binds Ca(2+) or phospholipids efficiently. Crystallography reveals that changes in the orientations of critical Ca(2+) ligands, and perhaps their flexibility, render the rat synaptotagmin 4 C(2)B domain unable to form full Ca(2+)-binding sites. These results indicate that synaptotagmin 4 is a Ca(2+) sensor in the fly but not in the rat, that the Ca(2+)-binding properties of C(2) domains cannot be reliably predicted from sequence analyses, and that proteins clearly identified as orthologs may nevertheless have markedly different functional properties.

• Pang T, Hisamitsu T, Mori H, Shigekawa M, Wakabayashi S
• Role of calcineurin B homologous protein in pH regulation by the Na+/H+ exchanger 1: tightly bound Ca2+ ions as important structural elements.
• Biochemistry. 2004; 43: 3628-36
• Display abstract

• We studied the role of the interaction of calcineurin homologous protein 1 (CHP1) with the Na(+)/H(+) exchanger 1 (NHE1), particularly its EF-hand Ca(2+) binding motifs, in the intracellular pH (pH(i))-dependent regulation of NHE1. We found that (45)Ca(2+) binds to two EF-hand motifs (EF3 and 4) of the recombinant CHP1 proteins with high affinity (apparent K(d) = approximately 90 nM). Complex formation between CHP1 and the CHP1 binding domain of NHE1 resulted in a marked increase in the Ca(2+) binding affinity (K(d) = approximately 2 nM) by promoting a conformational change of the EF-hands toward the tightly Ca(2+)-bound form. This suggests that CHP1 always contains two Ca(2+) ions when associated with NHE1 in cells. Interestingly, overexpression of GFP-tagged CHP1 with mutations in EF3 or EF4 significantly reduced the exchange activity in the neutral pH(i) range and partly impaired the activation of NHE1 in response to various stimuli, such as growth factors and osmotic stress. Furthermore, we found that, in addition to reducing the activity (V(max)), a CHP1 binding-defective NHE1 mutant had a marked reduction in pH(i) sensitivity ( approximately 0.7 pH unit acidic shift), which consequently abolished various regulatory responses of NHE1. These observations suggest that the association of NHE1 with CHP1 is crucial for maintenance of the pH(i) sensitivity of NHE1 and that tightly bound Ca(2+) ions may serve as important structural elements in the "pH(i) sensor" of NHE1.

• Rigden DJ, Galperin MY
• The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution.
• J Mol Biol. 2004; 343: 971-84
• Display abstract

• Calcium ions regulate many cellular processes and have important structural roles in living organisms. Despite the great variety of calcium-binding proteins (CaBPs), many of them contain the same Ca(2+)-binding helix-loop-helix structure, referred to as the EF-hand. In the canonical EF-hand, the loop contains three calcium-binding aspartic acid residues, which form the DxDxDG sequence motif, and is flanked by two alpha-helices. Recently, other CaBPs containing the same motif, but lacking one or both helices, have been described. Here, structural motif searches were used to analyse the full diversity of structural context in the known set of DxDxDG-containing CaBPs, including those where the structural resemblance of a given DxDxDG motif to that of EF-hands had not been noted. The results obtained indicate that the EF-hand represents but one, among many, structural context for the DxDxDG-like Ca(2+)-binding loops. While the structural similarity of the binuclear calcium-binding sites in anthrax protective antigen and human thrombospondin suggests that they are homologous, evolutionary relationships for mononuclear sites are harder to discern. The possible scenarios for the evolution of DxDxDG motif-containing calcium-binding loops in a variety of non-homologous proteins suggested loop transplant as a mechanism perhaps responsible for much of the diversity in structural contexts of present day DxDxDG-type CaBPs. Additionally, while it can be shown that existence of a DxDxDG sequence is not enough to confer a conformation suitable for calcium binding, local convergent evolution may still have a role. The analysis presented here has consequences for the prediction of calcium binding from sequence alone.

• Chakrabarty P et al.
• Identification and characterization of EhCaBP2. A second member of the calcium-binding protein family of the protozoan parasite Entamoeba histolytica.
• J Biol Chem. 2004; 279: 12898-908
• Display abstract

• Entamoeba histolytica, an early branching eukaryote, is the etiologic agent of amebiasis. Calcium plays a pivotal role in the pathogenesis of amebiasis by modulating the cytopathic properties of the parasite. However, the mechanistic role of Ca(2+) and calcium-binding proteins in the pathogenesis of E. histolytica remains poorly understood. We had previously characterized a novel calcium-binding protein (EhCaBP1) from E. histolytica. Here, we report the identification and partial characterization of an isoform of this protein, EhCaBP2. Both EhCaBPs have four canonical EF-hand Ca(2+) binding domains. The two isoforms are encoded by genes of the same size (402 bp). Comparison between the two genes showed an overall identity of 79% at the nucleotide sequence level. This identity dropped to 40% in the 75-nucleotide central linker region between the second and third Ca(2+) binding domains. Both of these genes are single copy, as revealed by Southern hybridization. Analysis of the available E. histolytica genome sequence data suggested that the two genes are non-allelic. Homology-based structural modeling showed that the major differences between the two EhCaBPs lie in the central linker region, normally involved in binding target molecules. A number of studies indicated that EhCaBP1 and EhCaBP2 are functionally different. They bind different sets of E. histolytica proteins in a Ca(2+)-dependent manner. Activation of endogenous kinase was also found to be unique for the two proteins and the Ca(2+) concentration required for their optimal functionality was also different. In addition, a 12-mer peptide was identified from a random peptide library that could differentially bind the two proteins. Our data suggest that EhCaBP2 is a new member of a class of E. histolytica calcium-binding proteins involved in a novel calcium signal transduction pathway.

• Iwasaki W, Sasaki H, Nakamura A, Kohama K, Tanokura M
• Metal-free and Ca2+-bound structures of a multidomain EF-hand protein, CBP40, from the lower eukaryote Physarum polycephalum.
• Structure. 2003; 11: 75-85
• Display abstract

• Acellular slime mold, Physarum polycephalum, has a unique wound-healing system. When cytoplasm of plasmodia is exposed to extracellular fluid, calcium binding protein 40 (CBP40) seals damaged areas, forming large aggregates Ca(2+) dependently. Part of the CBP40 is truncated at the N terminus by a proteinase in plasmodia (CBP40delta), which does not aggregate in the Ca(2+)-bound form. Here we report the crystal structures of CBP40delta in both the metal-free and the Ca(2+)-bound states. Both structures consist of three domains: coiled-coil, intervening, and EF-hand. The topology of the EF-hand domain is similar to that of calpain. The N-terminal half of CBP40Delta interacts with the C-terminal EF-hands through a large hydrophobic interface, necessary for high Ca(2+) affinity. Conformational change upon Ca(2+) binding is small; however, the structure of CBP40delta provides novel insights into the mechanism of Ca(2+)-dependent oligomerization.

• Yap KL, Ames JB, Swindells MB, Ikura M
• Vector geometry mapping. A method to characterize the conformation of helix-loop-helix calcium-binding proteins.
• Methods Mol Biol. 2002; 173: 317-24

• Michiels J, Xi C, Verhaert J, Vanderleyden J
• The functions of Ca(2+) in bacteria: a role for EF-hand proteins?
• Trends Microbiol. 2002; 10: 87-93
• Display abstract

• In bacteria, Ca(2+) is implicated in a wide variety of cellular processes, including the cell cycle and cell division. Dedicated influx and efflux systems tightly control the low cytoplasmic Ca(2+) levels in prokaryotes. Additionally, the growing number of proteins containing various Ca(2+)-binding motifs supports the importance of Ca(2+), which controls various protein functions by affecting protein stability, enzymatic activity or signal transduction. The existence of calmodulin-like proteins (containing EF-hand motifs) in bacteria is a long-standing hypothesis. Analysis of the prokaryotic protein sequences available in the databases has revealed the presence of several calmodulin-like proteins containing two or more authentic EF-hand motifs, suggesting that calmodulin-like proteins could be involved in Ca(2+) regulation in bacteria.

• Wang S et al.
• Cloning, characterization, and expression of calcyphosine 2, a novel human gene encoding an EF-hand Ca(2+)-binding protein.
• Biochem Biophys Res Commun. 2002; 291: 414-20
• Display abstract

• Calcyphosine is a calcium-binding protein containing four EF-hand domains, initially identified as thyroid protein p24. It was first cloned and its counterparts in rabbit, human, and mouse, crayfish and lobster of invertebrate were also cloned. Here we describe the cloning and characterization of a novel human calcyphosine gene. The 3829-bp cDNA encodes a EF-hand Ca(2+)-binding protein homologous to the dog calcyphosine. It also contains two EF-hand Ca(2+)-binding motif. It is abundantly expressed in many tissues including by RT-PCR analysis and believed to play important role in calcium signaling. It was mapped to human genome 12q15.

• Sugita S, Ho A, Sudhof TC
• NECABs: a family of neuronal Ca(2+)-binding proteins with an unusual domain structure and a restricted expression pattern.
• Neuroscience. 2002; 112: 51-63
• Display abstract

• Ca(2+)-signalling plays a major role in regulating all aspects of neuronal function. Different types of neurons exhibit characteristic differences in the responses to Ca(2+)-signals. Correlating with differences in Ca(2+)-response are expression patterns of Ca(2+)-binding proteins that often serve as markers for various types of neurons. For example, in the cerebral cortex the EF-hand Ca(2+)-binding proteins parvalbumin and calbindin are primarily expressed in inhibitory interneurons where they influence Ca(2+)-dependent responses. We have now identified a new family of proteins called NECABs (neuronal Ca(2+)-binding proteins). NECABs contain an N-terminal EF-hand domain that binds Ca(2+), but different from many other neuronal EF-hand Ca(2+)-binding proteins, only a single EF-hand domain is present. At the C-terminus, NECABs include a DUF176 motif, a bacterial domain of unknown function that was previously not observed in eukaryotes. In rat at least three closely related NECAB genes are expressed either primarily in brain (NECABs 1 and 2) or in brain and muscle (NECAB 3). Immunocytochemistry revealed that NECAB 1 is restricted to subsets of neurons. In cerebral cortex, NECAB 1 is highly and uniformly expressed only in layer 4 pyramidal neurons, whereas in hippocampus only inhibitory interneurons and CA2 pyramidal cells contain NECAB 1. In these neurons, NECAB 1 fills the entire cytoplasm similar to other EF-hand Ca(2+)-binding proteins, and is not concentrated in any particular subcellular compartment. We suggest that NECABs represent a novel family of regulatory Ca(2+)-binding proteins with an unusual domain structure and a limited expression in a subclass of neurons.

• Day IS, Reddy VS, Shad Ali G, Reddy AS
• Analysis of EF-hand-containing proteins in Arabidopsis.
• Genome Biol. 2002; 3: 56-56
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• BACKGROUND: In plants, calcium (Ca2+) has emerged as an important messenger mediating the action of many hormonal and environmental signals, including biotic and abiotic stresses. Many different signals raise cytosolic calcium concentration ([Ca2+]cyt), which in turn is thought to regulate cellular and developmental processes via Ca2+-binding proteins. Three out of the four classes of Ca2+-binding proteins in plants contain Ca2+-binding EF-hand motif(s). This motif is a conserved helix-loop-helix structure that can bind a single Ca2+ ion. To identify all EF-hand-containing proteins in Arabidopsis, we analyzed its completed genome sequence for genes encoding EF-hand-containing proteins. RESULTS: A maximum of 250 proteins possibly having EF-hands were identified. Diverse proteins, including enzymes, proteins involved in transcription and translation, protein- and nucleic-acid-binding proteins and a large number of unknown proteins, have one or more putative EF-hands. Phylogenetic analysis identified six major groups that contain some families of proteins. CONCLUSIONS: The presence of EF-hand motif(s) in a diversity of proteins is consistent with the involvement of Ca2+ in regulating many cellular and developmental processes. Thus far, only 47 of the possible 250 EF-hand proteins have been reported in the literature. Various domains that we identified in many of the uncharacterized EF-hand-containing proteins should help in elucidating their cellular role(s). Our analyses suggest that the Ca2+ messenger system is widely used in plants and that EF-hand-containing proteins are likely to be the key transducers mediating Ca2+ action.

• Atkinson RA et al.
• Ca2+-independent binding of an EF-hand domain to a novel motif in the alpha-actinin-titin complex.
• Nat Struct Biol. 2001; 8: 853-7
• Display abstract

• The interaction between alpha-actinin and titin, two modular muscle proteins, is essential for sarcomere assembly. We have solved the solution structure of a complex between the calcium-insensitive C-terminal EF-hand domain of alpha-actinin-2 and the seventh Z-repeat of titin. The structure of the complex is in a semi-open conformation and closely resembles that of myosin light chains in their complexes with heavy chain IQ motifs. However, no IQ motif is present in the Z-repeat, suggesting that the semi-open conformation is a general structural solution for calcium-independent recognition of EF-hand domains.

• Yonekawa T, Ohnishi Y, Horinouchi S
• A calcium-binding protein with four EF-hand motifs in Streptomyces ambofaciens.
• Biosci Biotechnol Biochem. 2001; 65: 156-60
• Display abstract

• A gene (cabA) encoding a calcium-binding protein was cloned from Streptomyces ambofaciens. CabA was 180 amino acid residues long and contained four typical EF-hand motifs bearing high sequence similarity to the calcium-binding sites in calmodulin. Consistent with this, CabA showed distinct calcium-binding activity, comparable to bovine brain calmodulin. cabA was transcribed throughout growth, as found by S1 nuclease mapping. Southern hybridization experiments showed that a single copy of cabA was present in various Streptomyces species. A hypothetical relationship between CabA and aerial mycelium formation in this strain was examined, since S. ambofaciens showed calcium-dependent aerial mycelium formation. However, disruption of cabA or overexpression of cabA in S. ambofaciens caused no detectable phenotypic changes.

• Yang K
• Prokaryotic calmodulins: recent developments and evolutionary implications.
• J Mol Microbiol Biotechnol. 2001; 3: 457-9
• Display abstract

• Ca2+ is a common intracellular second-messenger molecule in eukaryotic cells and regulates a myriad of cellular processes. Many effects of Ca2+ are mediated by calcium-binding regulatory proteins of the calmodulin superfamily. We propose the idea that calcium-binding proteins originated in high G+C Gram-positive bacteria and were later acquired by eukaryotes.

• Welch JT, Sirish M, Lindstrom KM, Franklin SJ
• De novo nucleases based on HTH and EF-hand chimeras.
• Inorg Chem. 2001; 40: 1982-4

• Felleisen RS, Hemphill A, Gottstein B
• A novel EF-hand calcium-binding protein in the flagellum of the protozoan Tritrichomonas suis.
• Parasitology. 2001; 122: 125-32
• Display abstract

• The cloning and characterization of Ts-p41, an EF-hand calcium-binding protein of the protozoan parasite Tritrichomonas suis is described. A T. suis cDNA library was screened with monospecific antibodies affinity purified on an immunoreactive 41 kDa antigen in a Triton X-114 membrane-protein fraction. The resulting cDNA fragments turned out to be derived from 2 different genes encoding closely related Ts-p41 variants. The deduced amino acid sequences contained 6 EF-hand domains perfectly matching the canonical consensus motif and a putative C-terminal prenylation site. Northern and Southern hybridizations revealed that Ts-p41 was highly expressed and encoded by a gene-family. A cDNA encoding Ts-p41 was expressed as recombinant protein in Escherichia coli. By overlay with 45Ca it was demonstrated that the native and recombinant Ts-p41 proteins bind Ca2+. In immunofluorescence, epitopes recognized by anti-Ts-p41 antibodies were distributed as well on the anterior flagella as on the recurrent flagellum of the parasite. Our findings with the parabasalid T. suis suggest that multiple EF-hand bearing calcium-binding proteins might be a common phenomenon associated with flagellar motility.

• Gribenko AV, Hopper JE, Makhatadze GI
• Molecular characterization and tissue distribution of a novel member of the S100 family of EF-hand proteins.
• Biochemistry. 2001; 40: 15538-48
• Display abstract

• We have isolated from a human prostate cDNA library a cDNA encoding a novel member of the S100 family of EF-hand proteins. The encoded 99-amino acid protein, designated S100Z, is capable of interacting with another member of the family, S100P. S100Z cDNA was cloned into a bacterial expression system, and the S100Z protein was purified to homogeneity from bacterial lysates by a combination of hydrophobic column and gel-filtration chromatography. Direct amino acid sequencing of the 20 N-terminal amino acids confirmed that the sequence of the recombinant protein is identical to the sequence deduced from the cDNA. Low-resolution structural data have been obtained using circular dichroism and fluorescence spectroscopies, and equilibrium analytical centrifugation. These results show that S100Z is a dimeric, predominantly alpha-helical protein. Addition of calcium to a solution of S100Z changes the fluorescence intensity of the protein, indicating that S100Z is capable of binding calcium ions. Analysis of the calcium-binding isotherm indicates the existence of two calcium-binding sites with apparent affinities on the order of 5 x 10(6) and 10(2) M(-1). Binding of calcium results in conformational changes and exposure of hydrophobic surfaces on the protein. Using a PCR-based assay, we have detected differences in the expression level of S100Z mRNA in various tissues. The highest levels were found in spleen and leukocytes. S100Z gene expression appears to be deregulated in some tumor tissues, compared to expression in their normal counterparts.

• Xie X, Dwyer MD, Swenson L, Parker MH, Botfield MC
• Crystal structure of calcium-free human sorcin: a member of the penta-EF-hand protein family.
• Protein Sci. 2001; 10: 2419-25
• Display abstract

• Sorcin is a 22 kD calcium-binding protein that is found in a wide variety of cell types, such as heart, muscle, brain and adrenal medulla. It belongs to the penta-EF-hand (PEF) protein family, which contains five EF-hand motifs that associate with membranes in a calcium-dependent manner. Prototypic members of this family are the calcium-binding domains of calpain, such as calpain dVI. Full-length human sorcin has been crystallized in the absence of calcium and the structure determined at 2.2 A resolution. Apart from an extended N-terminal portion, the sorcin molecule has a globular shape. The C-terminal domain is predominantly alpha-helical, containing eight alpha-helices and connecting loops incorporating five EF hands. Sorcin forms dimers through the association of the unpaired EF5, confirming this as the mode of association in the dimerization of PEF proteins. Comparison with calpain dVI reveals that the general folds of the individual EF-hand motifs are conserved, especially that of EF1, the novel EF-hand motif characteristic of the family. Detailed structural comparisons of sorcin with other members of PEF indicate that the EF-hand pair EF1-EF2 is likely to correspond to the two physiologically relevant calcium-binding sites and that the calcium-induced conformational change may be modest and localized within this pair of EF-hands. Overall, the results derived from the structural observations support the view that, in sorcin, calcium signaling takes place through the first pair of EF-hands.

• Springer TA, Jing H, Takagi J
• A novel Ca2+ binding beta hairpin loop better resembles integrin sequence motifs than the EF hand.
• Cell. 2000; 102: 275-7

• Yap KL, Ames JB, Swindells MB, Ikura M
• Diversity of conformational states and changes within the EF-hand protein superfamily.
• Proteins. 1999; 37: 499-507
• Display abstract

• The EF-hand motif, which assumes a helix-loop-helix structure normally responsible for Ca2+ binding, is found in a large number of functionally diverse Ca2+ binding proteins collectively known as the EF-hand protein superfamily. In many superfamily members, Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. In calmodulin and troponin C, this is described as a change from the closed conformational state in the absence of Ca2+ to the open conformational state in its presence. It is now clear from structures of other EF-hand proteins that this "closed-to-open" conformational transition is not the sole model for EF-hand protein structural response to Ca2+. More complex modes of conformational change are observed in EF-hand proteins that interact with a covalently attached acyl group (e.g., recoverin) and in those that dimerize (e.g., S100B, calpain). In fact, EF-hand proteins display a multitude of unique conformational states, together constituting a conformational continuum. Using a quantitative 3D approach termed vector geometry mapping (VGM), we discuss this tertiary structural diversity of EF-hand proteins and its correlation with target recognition.

• Dragani B, Aceto A
• About the role of conserved amino acid residues in the calcium-binding site of proteins.
• Arch Biochem Biophys. 1999; 368: 211-3

• Kawasaki H, Nakayama S, Kretsinger RH
• Classification and evolution of EF-hand proteins.
• Biometals. 1998; 11: 277-95
• Display abstract

• Forty-five distinct subfamilies of EF-hand proteins have been identified. They contain from two to eight EF-hands that are recognizable by amino acid sequence as being statistically similar to other EF-hand domains. All proteins within one subfamily are congruent to one another, i.e. the dendrogram computed from one of the EF-hand domains is similar, within statistical error, to the dendrogram computed from another(s) domain. Thirteen subfamilies--including Calmodulin, Troponin C, Essential light chain, Regulatory light chain--referred to collectively as CTER, are congruent with one another. They appear to have evolved from a single ur-domain by two cycles of gene duplication and fusion. The subfamilies of CTER subsequently evolved by gene duplications and speciations. The remaining 32 subfamilies do not show such general patterns of congruence; however, some--such as S100, intestinal calcium binding protein (calbindin 9 kd), and trichohylin--do not form congruent clusters of subfamilies. Nearly all of the domains 1, 3, 5, and 7 are most similar to other ODD domains. Correspondingly the EVEN numbered domains of all 45 subfamilies most closely resemble EVEN domains of other subfamilies. Many sequence and chemical characteristics do not show systemic trends by subfamily or species of host organisms; such homoplasy is widespread. Eighteen of the subfamilies are heterochimeric; in addition to multiple EF-hands they contain domains of other evolutionary origins.

• Sengupta LK et al.
• Calcium-dependent metabolic regulations in prokaryotes indicate conserved nature of calmodulin gene.
• Indian J Exp Biol. 1998; 36: 136-47
• Display abstract

• Role of free calcium and calcium binding protein calmodulin as signal molecule in cellular regulation is well established in eukaryotes. However, reports on Ca(2+)-dependent processes and their inhibition by calcium and/or calmodulin antagonists indicate towards the presence of calmodulin in prokaryotes as well. The common evolutionary origin of pro- and eukaryotes and many examples of evolutionary conservation of structure and functions support the contention of such conservation of the role of Ca2+ and calmodulin. Eukaryotic calmodulin (CaM) contains four structurally and functionally similar Ca2+ domains named I, II, III and IV. Each Ca2+ binding loop consists of 12 amino acid residues with ligands arranged spatially to satisfy the octahedral symmetry of Ca2+ binding. Plant calmodulin differ from vertebrate ones in 13 to 14 amino acid positions of which nine occur at -COOH- terminal half. Differences between protozoan and mammalian CaM also occur mostly in the same half. Isolation and characterization, although to a little extent, of CaM-like proteins from bacteria and cyanobacteria and their comparison with CaMs from diverse origin suggest high degree of conservation. Non-bulky amino acids like glycine, alanine and serine with low specific rotation are present in greater number in the primitive form of calmodulin and have been significantly reduced in highly evolved form of calmodulin, suggesting that their requirement was insignificant and were eliminated from EF hand structure during evolution. However, amino acids like glutamate/glutamine and aspartate/asparagine were highly conserved and did not show any major change in their frequency since their positions are too significant in calcium binding domain. While the number of positively charged amino acids like arginine and leucine was increased, histidine containing weakly ionized group and having a significant buffering capacity was reduced to a major extent, further suggesting that the acidic nature of calmodulin protein has been maintained during evolution. Thus it is now clear that the entire superfamily of Ca2+ binding proteins have arisen from a common genetic ancestry. Two successive tandem duplications of gene encoding a single domain containing protein of 30-40 residues gave rise to a four domain molecule from which this family was then derived.

• Rodrigues JJ, Ferreira HB, Farias SE, Zaha A
• A protein with a novel calcium-binding domain associated with calcareous corpuscles in Echinococcus granulosus.
• Biochem Biophys Res Commun. 1997; 237: 451-6
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• A novel intracellular calcium-binding protein from Echinococcus granulosus is described in this work. A cDNA was isolated from a lambdagt11 protoscolex expression library and the deduced amino acid sequence has at least fifteen sequentially repeated twelve-residue repeats that resemble the calcium-binding loop of EF-hands; however, the dodecamer motif has no flanking helices. The cDNA was expressed in Escherichia coli using the pGEX vector, and a recombinant fusion protein (EgCaBP1-GST) was obtained. The recombinant fusion protein binds calcium when assayed with 45Ca. It is possible that the calcium-binding motifs present a secondary structure similar to the parallel beta roll structure described for an alkaline protease from Pseudomonas aeruginosa. A native protein of more than 300 kDa was recognized by an anti-EgCaBP1 monoclonal antibody by Western-blot analysis. Immunohistochemistry using a pool of anti-EgCaBP1-GST mouse sera demonstrated a strong association of the protein with calcareous corpuscles. The possible role of this protein and that of the calcareous corpuscles in the protoscolex are discussed.

• Ikura M
• Calcium binding and conformational response in EF-hand proteins.
• Trends Biochem Sci. 1996; 21: 14-7
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• EF-hand proteins undergo conformational changes upon binding of Ca2+. This event is a crucial step in many Ca2+-dependent cellular processes. Recent advances in the three-dimensional structural analysis of various EF-hand proteins have led to new insights into the structure and functional relationship of this large family of Ca2+-binding proteins.

• Maurer P, Hohenester E, Engel J
• Extracellular calcium-binding proteins.
• Curr Opin Cell Biol. 1996; 8: 609-17
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• Point mutations in Ca2+-binding sites of extracellular matrix proteins have been identified as the cause of human disorders such as Marfansyndrome and pseudoachondroplasia. Although the modes of Ca2+ binding and the effects of point mutations are not yet understood in these two cases, new insight was recently gained by X-ray and NMR structure determinations of several other extracellular proteins; these studies revealed a diversity of functions of Ca2+ ions. Ca2+ may induce a profound conformational change within a single domain, may bridge adjacent domains and thus direct the relative domain orientation and supramolecular structure, or may be involved in carbohydrate and membrane binding.

• Presland RB, Bassuk JA, Kimball JR, Dale BA
• Characterization of two distinct calcium-binding sites in the amino-terminus of human profilaggrin.
• J Invest Dermatol. 1995; 104: 218-23
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• Profilaggrin is a large phosphorylated protein (approximately 400 kDa in humans) that is expressed in the granular cells of epidermis where it forms a major component of keratohyalin. It consists of multiple copies of similar filaggrin units plus amino- and carboxy-terminal domains that differ from filaggrin. Proteolytic processing of profilaggrin during terminal differentiation results in the removal of these domains and generation of monomeric filaggrin units, which associate with keratin intermediate filaments to form macrofibrils in the stratum corneum. The amino-terminal domain contains two calcium-binding motifs similar to the EF-hands found in the S-100 family of calcium-binding proteins. In this report, we expressed the 293-residue amino-terminal pro-domain of human profilaggrin as a polyhistidine fusion protein in Escherichia coli, and characterized calcium binding by a 45Ca++ binding assay and fluorescence emission spectroscopy. Fluorescence measurements indicated that the profilaggrin polypeptide undergoes conformational changes upon the removal of Ca++ with ethylenediamine tetraacetic acid, demonstrating the presence of two calcium-binding sites with affinities for calcium that differ ninefold (1.4 x 10(-4) M and 1.2 x 10(-3) M). We suggest that this functional calcium-binding domain at the amino-terminus of human profilaggrin plays a role in profilaggrin processing and in other calcium-dependent processes during terminal differentiation of the epidermis.

• Gomes AV, Barnes JA
• Pest sequences in EF-hand calcium-binding proteins.
• Biochem Mol Biol Int. 1995; 37: 853-60
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• Calcium binding proteins are subdivided into two major families: the EF-family and the Annexin family. The EF-hand family is distinguished by the characteristic helix-loop-helix motif which consists of two alpha-helices separated by a loop. The EF-hand Ca2+(-)binding protein family contain subfamilies rich in proline, glutamic acid, serine and threonine residues (called PEST sequences) and non PEST-containing subfamilies. A few of the Ca2+(-)binding proteins contain KFERQ-like sequences which are thought to be possible signals for lysosomal degradation. Arginine pairs (RR) which have also been suggested to act as signals for proteolysis were found to be few or absent. However, most EF-hand proteins were found to possess lysine pairs (KK) which may also act as signals for proteolysis.

• Nakayama S, Kretsinger RH
• Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism.
• J Mol Evol. 1993; 36: 458-76
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• In the first report in this series we presented dendrograms based on 152 individual proteins of the EF-hand family. In the second we used sequences from 228 proteins, containing 835 domains, and showed that eight of the 29 subfamilies are congruent and that the EF-hand domains of the remaining 21 subfamilies have diverse evolutionary histories. In this study we have computed dendrograms within and among the EF-hand subfamilies using the encoding DNA sequences. In most instances the dendrograms based on protein and on DNA sequences are very similar. Significant differences between protein and DNA trees for calmodulin remain unexplained. In our fourth report we evaluate the sequences and the distribution of introns within the EF-hand family and conclude that exon shuffling did not play a significant role in its evolution.

• Kretsinger RH, Moncrief ND
• Evolution of calcium modulated proteins.
• Va Explor. 1989; 5: 7-9

• Franke WW
• Homology of a conserved sequence in the tail domain of intermediate filament proteins with the loop region of calcium binding proteins.
• Cell Biol Int Rep. 1987; 11: 831-831

• Ennever J, Vogel J, Takazoe I
• Calcium binding by a lipid extract of Bacterionema matruchotii.
• Calcif Tissue Res. 1968; 2: 296-8

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