Secondary literature sources for MeTrc
The following references were automatically generated.
- Perduca M, Mancia F, Del Giorgio R, Monaco HL
- Crystal structure of a truncated form of porcine odorant-binding protein.
- Proteins. 2001; 42: 201-9
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The odorant-binding proteins (OBPs) are a family of structurally related molecules that are found in high concentrations in the nasal mucus of vertebrates and bind with moderate affinity a large family of hydrophobic odorants. On the basis of their quaternary structure, the OBPs have been classified as monomers, homodimers, and heterodimers. Porcine OBP was believed for a long time to be a monomer under physiological conditions but there are recent data that support the existence of a monomer-dimer equilibrium. We have determined the crystal structure of a monoclinic form of porcine OBP and found that the truncated molecules, which lack the first 8 amino acids, pack in the cell as dimers that appear to have physiological relevance. The presence in the maps of electron density for an endogenous ligand has also let us identify the side chain of the amino acids that are at the ligand-binding site. In addition, an alternative way of access to the central cavity that binds the ligands is suggested by the particular packing of the molecules in this unit cell. Proteins 2001;42:201-209.
- Zubieta C, He XZ, Dixon RA, Noel JP
- Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases.
- Nat Struct Biol. 2001; 8: 271-9
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Chalcone O-methyltransferase (ChOMT) and isoflavone O-methyltransferase (IOMT) are S-adenosyl-l-methionine (SAM) dependent plant natural product methyltransferases involved in secondary metabolism in Medicago sativa (alfalfa). Here we report the crystal structure of ChOMT in complex with the product S-adenosyl-l-homocysteine and the substrate isoliquiritigenin (4,2',4'-trihydroxychalcone) refined to 1.8 A as well as the crystal structure of IOMT in complex with the products S-adenosyl-l-homocysteine and isoformononetin (4'-hydroxy-7-methoxyisoflavone) refined to 1.4 A. These two OMTs constitute the first plant methyltransferases to be structurally characterized and reveal a novel oligomerization domain and the molecular determinants for substrate selection. As such, this work provides a structural basis for understanding the substrate specificity of the diverse family of plant OMTs and facilitates the engineering of novel activities in this extensive class of natural product biosynthetic enzymes.
- Barnakov AN, Barnakova LA, Hazelbauer GL
- Location of the receptor-interaction site on cheb, the methylesterase response regulator of bacterial chemotaxis.
- J Biol Chem. 2001; 276: 32984-9
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Sensory adaptation in bacterial chemotaxis is mediated by covalent modification of chemoreceptors, specifically methylation and demethylation of glutamates catalyzed by methyltransferase CheR and methylesterase CheB. The methylesterase is a two-domain response regulator in which phosphorylation of the regulatory domain enhances activity of the catalytic domain. In Escherichia coli and Salmonella typhimurium, a crucial determinant of efficient methylation and demethylation is a specific pentapeptide sequence at the chemoreceptor carboxyl terminus, a position distant from sites of enzymatic action. Each enzyme binds pentapeptide, but the site of binding has been located only for CheR. Here we locate the pentapeptide-binding site on CheB by assessing catalytic activity and pentapeptide binding of CheB fragments, protection of CheB from proteolysis by pentapeptide, and interference with pentapeptide-CheB interaction by a CheB segment. The results place the binding site near the hinge between regulatory and catalytic domains, in a segment spanning the carboxyl-terminal end of the regulatory domain and the beginning of the linker that stretches to the catalytic domain. This location is quite different from the catalytic domain location of the pentapeptide-binding site on CheR and is likely to reflect the rather different ways in which pentapeptide binding enhances enzymatic action for the methyltransferase and the methylesterase.
- Ha S, Walker D, Shi Y, Walker S
- The 1.9 A crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis.
- Protein Sci. 2000; 9: 1045-52
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The 1.9 A X-ray structure of a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis is reported. This enzyme, MurG, contains two alpha/beta open sheet domains separated by a deep cleft. Structural analysis suggests that the C-terminal domain contains the UDP-GlcNAc binding site while the N-terminal domain contains the acceptor binding site and likely membrane association site. Combined with sequence data from other MurG homologs, this structure provides insight into the residues that are important in substrate binding and catalysis. We have also noted that a conserved region found in many UDP-sugar transferases maps to a beta/alpha/beta/alpha supersecondary structural motif in the donor binding region of MurG, an observation that may be helpful in glycosyltransferase structure prediction. The identification of a conserved structural motif involved in donor binding in different UDP-sugar transferases also suggests that it may be possible to identify--and perhaps alter--the residues that help determine donor specificity.
- Zhang X, Zhou L, Cheng X
- Crystal structure of the conserved core of protein arginine methyltransferase PRMT3.
- EMBO J. 2000; 19: 3509-19
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Protein arginine methylation has been implicated in signal transduction, nuclear transport and transcription regulation. Protein arginine methyltransferases (PRMTs) mediate the AdoMet-dependent methylation of many proteins, including many RNA binding proteins involved in various aspects of RNA processing and/or transport. Here we describe the crystal structure of the rat PRMT3 catalytic core in complex with reaction product AdoHcy, determined at 2.0 A resolution. The results reveal a two-domain structure: an AdoMet-binding domain and a barrel-like domain. The AdoMet-binding domain is a compact version of the consensus AdoMet-dependent methyltransferase fold. The active site is situated in a cone-shaped pocket between the two domains. The residues that make up the active site are conserved across the PRMT family, consisting of a double-E loop containing two invariant Glu and one His-Asp proton-relay system. The structure suggests a mechanism for the methylation reaction and provides the structural basis for functional characterization of the PRMT family. In addition, crystal packing and solution behavior suggest dimer formation of the PRMT3 core.
- Bugl H et al.
- RNA methylation under heat shock control.
- Mol Cell. 2000; 6: 349-60
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Structural, biochemical, and genetic techniques were applied to investigate the function of FtsJ, a recently identified heat shock protein. FtsJ is well conserved, from bacteria to humans. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. The molecular surface of FtsJ exposes a putative nucleic acid binding groove composed of highly conserved, positively charged residues. Substrate analysis showed that FtsJ methylates 23S rRNA within 50S ribosomal subunits in vitro and in vivo. Null mutations in ftsJ show a dramatically altered ribosome profile, a severe growth disadvantage, and a temperature-sensitive phenotype. Our results reveal an unexpected link between the heat shock response and RNA metabolism.
- Wang H, Boisvert D, Kim KK, Kim R, Kim SH
- Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution.
- EMBO J. 2000; 19: 317-23
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Fibrillarin is a phylogenetically conserved protein essential for efficient processing of pre-rRNA through its association with a class of small nucleolar RNAs during ribosomal biogenesis. The protein is the antigen for the autoimmune disease scleroderma. Here we report the crystal structure of the fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. The structure consists of two domains, with a novel fold in the N-terminal region and a methyltransferase-like domain in the C-terminal region. Mapping temperature-sensitive mutations found in yeast fibrillarin Nop1 to the Methanococcus homologue structure reveals that many of the mutations cluster in the core of the methyltransferase-like domain.
- Skinner MM, Puvathingal JM, Walter RL, Friedman AM
- Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair.
- Structure Fold Des. 2000; 8: 1189-201
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BACKGROUND: Formation of isoaspartyl residues is one of several processes that damage proteins as they age. Protein L-isoaspartate (D-aspartate) O-methyltransferase (PIMT) is a conserved and nearly ubiquitous enzyme that catalyzes the repair of proteins damaged by isoaspartyl formation. RESULTS: We have determined the first structure of a PIMT from crystals of the T. maritima enzyme complexed to S-adenosyl-L-homocysteine (AdoHcy) and refined it to 1.8 A resolution. Although PIMT forms one structural unit, the protein can be divided functionally into three subdomains. The central subdomain closely resembles other S-adenosyl-L-methionine-dependent methyltransferases but bears a striking alteration of topological connectivity, which is not shared by any other member of this family. Rather than arranged as a mixed beta sheet with topology 6 upward arrow7 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow, the central sheet of PIMT is reorganized to 7 upward arrow6 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow. AdoHcy is largely buried between the N-terminal and central subdomains by a conserved and largely hydrophobic loop on one rim of the binding cleft, and a conserved Ser/Thr-rich beta strand on the other. The Ser/Thr-rich strand may provide hydrogen bonds for specific interactions with isoaspartyl substrates. The side chain of Ile-206, a conserved residue, crosses the cleft, restricting access to the donor methyl group to a deep well, the putative isoaspartyl methyl acceptor site. CONCLUSIONS: The structure of PIMT reveals a unique modification of the methyltransferase fold along with a site for specific recognition of isoaspartyl substrates. The sequence conservation among PIMTs suggests that the current structure should prove a reliable model for understanding the repair of isoaspartyl damage in all organisms.
- Huang Y et al.
- Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes.
- J Mol Biol. 2000; 298: 149-62
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Glycine N-methyltransferase (S-adenosyl-l-methionine: glycine methyltransferase, EC 2.1.1.20; GNMT) catalyzes the AdoMet-dependent methylation of glycine to form sarcosine (N-methylglycine). Unlike most methyltransferases, GNMT is a tetrameric protein showing a positive cooperativity in AdoMet binding and weak inhibition by S-adenosylhomocysteine (AdoHcy). The first crystal structure of GNMT complexed with AdoMet showed a unique "closed" molecular basket structure, in which the N-terminal section penetrates and corks the entrance of the adjacent subunit. Thus, the apparent entrance or exit of the active site is not recognizable in the subunit structure, suggesting that the enzyme must possess a second, enzymatically active, "open" structural conformation. A new crystalline form of the R175K enzyme has been grown in the presence of an excess of AdoHcy, and its crystal structure has been determined at 3.0 A resolution. In this structure, the N-terminal domain (40 amino acid residues) of each subunit has moved out of the active site of the adjacent subunit, and the entrances of the active sites are now opened widely. An AdoHcy molecule has entered the site occupied in the "closed" structure by Glu15 and Gly16 of the N-terminal domain of the adjacent subunit. An AdoHcy binds to the consensus AdoMet binding site observed in the other methyltransferase. This AdoHcy binding site supports the glycine binding site (Arg175) deduced from a chemical modification study and site-directed mutagenesis (R175K). The crystal structures of WT and R175K enzymes were also determined at 2.5 A resolution. These enzyme structures have a closed molecular basket structure and are isomorphous to the previously determined AdoMet-GNMT structure. By comparing the open structure to the closed structure, mechanisms for auto-inhibition and for the forced release of the product AdoHcy have been revealed in the GNMT structure. The N-terminal section of the adjacent subunit occupies the AdoMet binding site and thus inhibits the methyltransfer reaction, whereas the same N-terminal section forces the departure of the potentially potent inhibitor AdoHcy from the active site and thus facilitates the methyltransfer reaction. Consequently GNMT is less active at a low level of AdoMet concentration, and is only weakly inhibited by AdoHcy. These properties of GNMT are particularly suited for regulation of the cellular AdoMet/AdoHcy ratio.
- Carr S, Penfold CN, Bamford V, James R, Hemmings AM
- The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9.
- Structure Fold Des. 2000; 8: 57-66
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BACKGROUND: E colicin proteins have three functional domains, each of which is implicated in one of the stages of killing Escherichia coli cells: receptor binding, translocation and cytotoxicity. The central (R) domain is responsible for receptor-binding activity whereas the N-terminal (T) domain mediates translocation, the process by which the C-terminal cytotoxic domain is transported from the receptor to the site of its cytotoxicity. The translocation of enzymatic E colicins like colicin E9 is dependent upon TolB but the details of the process are not known. RESULTS: We have demonstrated a protein-protein interaction between the T domain of colicin E9 and TolB, an essential component of the tol-dependent translocation system in E. coli, using the yeast two-hybrid system. The crystal structure of TolB, a procaryotic tryptophan-aspartate (WD) repeat protein, reveals an N-terminal alpha + beta domain based on a five-stranded mixed beta sheet and a C-terminal six-bladed beta-propeller domain. CONCLUSIONS: The results suggest that the TolB-box residues of the T domain of colicin E9 interact with the beta-propeller domain of TolB. The protein-protein interactions of other beta-propeller-containing proteins, the yeast yPrp4 protein and G proteins, are mediated by the loops or outer sheets of the propeller blades. The determination of the three-dimensional structure of the T domain-TolB complex and the isolation of mutations in TolB that abolish the interaction with the T domain will reveal fine details of the protein-protein interaction of TolB and the T domain of E colicins.
- Kubori T, Sukhan A, Aizawa SI, Galan JE
- Molecular characterization and assembly of the needle complex of the Salmonella typhimurium type III protein secretion system.
- Proc Natl Acad Sci U S A. 2000; 97: 10225-30
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Many bacterial pathogens of plants and animals have evolved a specialized protein-secretion system termed type III to deliver bacterial proteins into host cells. These proteins stimulate or interfere with host cellular functions for the pathogen's benefit. The Salmonella typhimurium pathogenicity island 1 encodes one of these systems that mediates this bacterium's ability to enter nonphagocytic cells. Several components of this type III secretion system are organized in a supramolecular structure termed the needle complex. This structure is made of discrete substructures including a base that spans both membranes and a needle-like projection that extends outward from the bacterial surface. We demonstrate here that the type III secretion export apparatus is required for the assembly of the needle substructure but is dispensable for the assembly of the base. We show that the length of the needle segment is determined by the type III secretion associated protein InvJ. We report that InvG, PrgH, and PrgK constitute the base and that PrgI is the main component of the needle of the type III secretion complex. PrgI homologs are present in type III secretion systems from bacteria pathogenic for animals but are absent from bacteria pathogenic for plants. We hypothesize that the needle component may establish the specificity of type III secretion systems in delivering proteins into either plant or animal cells.
- Muller-Dieckmann HJ, Grantz AA, Kim SH
- The structure of the signal receiver domain of the Arabidopsis thaliana ethylene receptor ETR1.
- Structure Fold Des. 1999; 7: 1547-56
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BACKGROUND: In Arabidopsis thaliana, ethylene perception and signal transduction into the cell are carried out by a family of membrane-bound receptors, one of which is ethylene resistant 1 (ETR1). The large cytoplasmic domain of the receptor showed significant sequence homology to the proteins of a common bacterial regulatory pathway, the two-component system. This system consists of a transmitter histidine kinase and a response regulator (or signal receiver). We present the crystal structures of the first plant receiver domain ETRRD (residues 604-738) of ETR1 in two conformations. RESULTS: The monomeric form of ETRRD resembles the known structure of the bacterial receiver domain. ETRRD forms a homodimer in solution and in the crystal, an interaction that has not been described previously. Dimerization is mediated by the C terminus, which forms an extended beta sheet with the dimer-related beta-strand core. Furthermore, the loop immediately following the active site adopts an exceptional conformation. CONCLUSIONS: The three-dimensional structure of ETRRD shows the expected conformational conservation to prokaryotic receiver proteins, such as CheY and CheB, both of which are part of the chemotaxis signaling pathway. ETRRD provides the first detailed example of a dimerized receiver domain. Given that the dimer interface of ETRRD coincides with the phosphorylation-dependent interfaces of CheY and CheB, we suggest that the monomerization of ETRRD is phosphorylation-dependent too. In the Mg(2+)-free form of ETRRD, the gamma-loop conformation does not allow a comparable interaction as observed in the active-site architectures of Mg(2+)-bound CheY from Escherichia coli and Salmonella typhimurium.
- Abergel C et al.
- Structure of the Escherichia coli TolB protein determined by MAD methods at 1.95 A resolution.
- Structure Fold Des. 1999; 7: 1291-300
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BACKGROUND: The periplasmic protein TolB from Escherichia coli is part of the Tol-PAL (peptidoglycan-associated lipoprotein) multiprotein complex used by group A colicins to penetrate and kill cells. TolB homologues are found in many gram-negative bacteria and the Tol-PAL system is thought to play a role in bacterial envelope integrity. TolB is required for lethal infection by Salmonella typhimurium in mice. RESULTS: The crystal structure of the selenomethionine-substituted TolB protein from E. coli was solved using multiwavelength anomalous dispersion methods and refined to 1. 95 A. TolB has a two-domain structure. The N-terminal domain consists of two alpha helices, a five-stranded beta-sheet floor and a long loop at the back of this floor. The C-terminal domain is a six-bladed beta propeller. The small, possibly mobile, contact area (430 A(2)) between the two domains involves residues from the two helices and the first and sixth blades of the beta propeller. All available genomic sequences were used to identify new TolB homologues in gram-negative bacteria. The TolB structure was then interpreted using the observed conservation pattern. CONCLUSIONS: The TolB beta-propeller C-terminal domain exhibits sequence similarities to numerous members of the prolyl oligopeptidase family and, to a lesser extent, to class B metallo-beta-lactamases. The alpha/beta N-terminal domain shares a structural similarity with the C-terminal domain of transfer RNA ligases. We suggest that the TolB protein might be part of a multiprotein complex involved in the recycling of peptidoglycan or in its covalent linking with lipoproteins.
- Ko TP, Liao CC, Ku WY, Chak KF, Yuan HS
- The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein.
- Structure Fold Des. 1999; 7: 91-102
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BACKGROUND: Colicin E7 (ColE7) is one of the bacterial toxins classified as a DNase-type E-group colicin. The cytotoxic activity of a colicin in a colicin-producing cell can be counteracted by binding of the colicin to a highly specific immunity protein. This biological event is a good model system for the investigation of protein recognition. RESULTS: The crystal structure of a one-to-one complex between the DNase domain of colicin E7 and its cognate immunity protein Im7 has been determined at 2.3 A resolution. Im7 in the complex is a varied four-helix bundle that is identical to the structure previously determined for uncomplexed Im7. The structure of the DNase domain of ColE7 displays a novel alpha/beta fold and contains a Zn2+ ion bound to three histidine residues and one water molecule in a distorted tetrahedron geometry. Im7 has a V-shaped structure, extending two arms to clamp the DNase domain of ColE7. One arm (alpha1(*)-loop12-alpha2(*); where * represents helices in Im7) is located in the region that displays the greatest sequence variation among members of the immunity proteins in the same subfamily. This arm mainly uses acidic sidechains to interact with the basic sidechains in the DNase domain of ColE7. The other arm (loop 23-alpha3(*)-loop 34) is more conserved and it interacts not only with the sidechain but also with the mainchain atoms of the DNase domain of ColE7. CONCLUSIONS: The protein interfaces between the DNase domain of ColE7 and Im7 are charge-complementary and charge interactions contribute significantly to the tight and specific binding between the two proteins. The more variable arm in Im7 dominates the binding specificity of the immunity protein to its cognate colicin. Biological and structural data suggest that the DNase active site for ColE7 is probably near the metal-binding site.
- Schluckebier G, Zhong P, Stewart KD, Kavanaugh TJ, Abad-Zapatero C
- The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism.
- J Mol Biol. 1999; 289: 277-91
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The rRNA methyltransferase ErmC' transfers methyl groups from S -adenosyl-l-methionine to atom N6 of an adenine base within the peptidyltransferase loop of 23 S rRNA, thus conferring antibiotic resistance against a number of macrolide antibiotics. The crystal structures of ErmC' and of its complexes with the cofactor S -adenosyl-l-methionine, the reaction product S-adenosyl-l-homocysteine and the methyltransferase inhibitor Sinefungin, respectively, show that the enzyme undergoes small conformational changes upon ligand binding. Overall, the ligand molecules bind to the protein in a similar mode as observed for other methyltransferases. Small differences between the binding of the amino acid parts of the different ligands are correlated with differences in their chemical structure. A model for the transition-state based on the atomic details of the active site is consistent with a one-step methyl-transfer mechanism and might serve as a first step towards the design of potent Erm inhibitors.
- Schubert HL, Wilson KS, Raux E, Woodcock SC, Warren MJ
- The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase.
- Nat Struct Biol. 1998; 5: 585-92
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Biosynthesis of the corrin ring of vitamin B12 requires the action of six S-adenosyl-L-methionine (AdoMet) dependent transmethylases, closely related in sequence. The first X-ray structure of one of these, cobalt-precorrin-4 transmethylase, CbiF, from Bacillus megaterium has been determined to a resolution of 2.4 A. CbiF contains two alphabeta domains forming a trough in which S-adenosyl-L-homocysteine (AdoHcy) binds. The location of AdoHcy and a number of conserved residues, helps define the precorrin binding site. A second crystal form determined at 3.1 A resolution highlights the flexibility of two loops around this site. CbiF employs a unique mode of AdoHcy binding and represents a new class of transmethylase.
- Bussiere DE et al.
- Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria.
- Biochemistry. 1998; 37: 7103-12
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The prevalent mechanism of bacterial resistance to erythromycin and other antibiotics of the macrolide-lincosamide-streptogramin B group (MLS) is methylation of the 23S rRNA component of the 50S subunit in bacterial ribosomes. This sequence-specific methylation is catalyzed by the Erm group of methyltransferases (MTases). They are found in several strains of pathogenic bacteria, and ErmC is the most studied member of this class. The crystal structure of ErmC' (a naturally occurring variant of ErmC) from Bacillus subtilis has been determined at 3.0 A resolution by multiple anomalous diffraction phasing methods. The structure consists of a conserved alpha/beta amino-terminal domain which binds the cofactor S-adenosyl-l-methionine (SAM), followed by a smaller, alpha-helical RNA-recognition domain. The beta-sheet structure of the SAM-binding domain is well-conserved between the DNA, RNA, and small-molecule MTases. However, the C-terminal nucleic acid binding domain differs from the DNA-binding domains of other MTases and is unlike any previously reported RNA-recognition fold. A large, positively charged, concave surface is found at the interface of the N- and C-terminal domains and is proposed to form part of the protein-RNA interaction surface. ErmC' exhibits the conserved structural motifs previously found in the SAM-binding domain of other methyltransferases. A model of SAM bound to ErmC' is presented which is consistent with the motif conservation among MTases.
- Forst D, Welte W, Wacker T, Diederichs K
- Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose.
- Nat Struct Biol. 1998; 5: 37-46
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The X-ray structure of a sucrose-specific porin (ScrY) from Salmonella typhimurium has been determined by multiple isomorphous replacement at 2.4 A resolution both in its uncomplexed form and with bound sucrose. ScrY is a noncrystallographic trimer of identical subunits, each with 413 structurally well-defined amino acids. A monomer is built up of 18 anti-parallel beta-strands surrounding a hydrophilic pore, with a topology closely similar to that of maltoporin. Two non-overlapping sucrose-binding sites were identified in difference Fourier maps. The higher permeability for sucrose of ScrY as compared to maltoporin is mainly accounted for by differences in their pore-lining residues.
- Turner MA, Yuan CS, Borchardt RT, Hershfield MS, Smith GD, Howell PL
- Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength.
- Nat Struct Biol. 1998; 5: 369-76
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S-Adenosylhomocysteine (AdoHcy) hydrolase regulates all adenosylmethionine-(AdoMet) dependent transmethylations by hydrolyzing the potent feedback inhibitor AdoHcy to homocysteine and adenosine. The crystallographic structure determination of a selenomethionyl-incorporated AdoHcy hydrolase inhibitor complex was accomplished using single wavelength anomalous diffraction data and the direct methods program, Snb v2.0, which produced the positions of all 30 crystallographically distinct selenium atoms. The mode of enzyme-cofactor binding is unique, requiring interactions from two protein monomers. An unusual dual role for a catalytic water molecule in the active site is revealed in the complex with the adenosine analog 2'-hydroxy, 3'-ketocyclopent-4'-enyladenine.
- Djordjevic S, Goudreau PN, Xu Q, Stock AM, West AH
- Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain.
- Proc Natl Acad Sci U S A. 1998; 95: 1381-6
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We report the x-ray crystal structure of the methylesterase CheB, a phosphorylation-activated response regulator involved in reversible modification of bacterial chemotaxis receptors. Methylesterase CheB and methyltransferase CheR modulate signaling output of the chemotaxis receptors by controlling the level of receptor methylation. The structure of CheB, which consists of an N-terminal regulatory domain and a C-terminal catalytic domain joined by a linker, was solved by molecular replacement methods using independent search models for the two domains. In unphosphorylated CheB, the N-terminal domain packs against the active site of the C-terminal domain and thus inhibits methylesterase activity by directly restricting access to the active site. We propose that phosphorylation of CheB induces a conformational change in the regulatory domain that disrupts the domain interface, resulting in a repositioning of the domains and allowing access to the active site. Structural similarity between the two companion receptor modification enzymes, CheB and CheR, suggests an evolutionary and/or functional relationship. Specifically, the phosphorylated N-terminal domain of CheB may facilitate interaction with the receptors, similar to the postulated role of the N-terminal domain of CheR. Examination of surfaces in the N-terminal regulatory domain of CheB suggests that despite a common fold throughout the response regulator family, surfaces used for protein-protein interactions differ significantly. Comparison between CheB and other response regulators indicates that analogous surfaces are used for different functions and conversely, similar functions are mediated by different molecular surfaces.
- Ogawa H, Gomi T, Takusagawa F, Fujioka M
- Structure, function and physiological role of glycine N-methyltransferase.
- Int J Biochem Cell Biol. 1998; 30: 13-26
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Glycine N-methyltransferase (EC 2.1.1.20) catalyzes the transfer of the methyl group of S-adenosylmethionine (AdoMet) to glycine to form S-adenosylhomocysteine and sarcosine. Unlike most AdoMet-dependent methyltransferases, glycine N-methyltransferase is a tetramer of identical subunits. Crystallography of recombinant rat glycine N-methyltransferase indicates that four nearly spherical subunits are arranged to form a flat, square tetramer with a large hole in the centre. The enzyme occurs abundantly in the livers of rat, rabbit and mouse. Glycine N-methyltransferases from rat, rabbit, human and pig livers are shown to have similar amino acid sequences and, with the enzymes from rat and rabbit livers, it is demonstrated that the N-terminal valine is acetylated. Glycine N-methyltransferases from livers exhibit sigmoidal rate behaviour with respect to AdoMet and hyperbolic behaviour with respect to glycine at all pH tested. However, recombinant rat glycine N-methyltransferase which lacks the N-terminal acetyl group shows no cooperativity toward AdoMet at neutral pH, suggesting that elimination of the positive charge at the N-terminus is required for cooperative behaviour. Glycine N-methyltransferase binds 5-methyltetrahydropteroylpentaglutamate tightly, resulting in inhibition of the catalytic activity. The nature of these unique functional features is discussed in the light of the three-dimensional structure of the enzyme. The tissue and subcellular localization of the enzyme and its possible role in methionine metabolism are reviewed.
- Wu J, Li J, Li G, Long DG, Weis RM
- The receptor binding site for the methyltransferase of bacterial chemotaxis is distinct from the sites of methylation.
- Biochemistry. 1996; 35: 4984-93
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The principal locus for binding interactions between the aspartate and serine receptors of escherichia coli and the methyltransferase was found to be in the last five amino acids of the receptor. The thermodynamic parameters of transferase-receptor interactions were determined by isothermal titration calorimetry. the serine receptor and three C-terminal fragments (C-fragments) of the aspartate receptor consisting of ether the last 297, 88, or 38 amino acids gave comparable values for binding (n=1, deltaH approximately 13 kcal/mol, and Ka approximately 4 x 10(5)M-1). Truncating either 16 or 36 amino acids form the C-terminus eliminated observable interactions. Finally the pentapeptide Asn-Trp-Glu-Thr-Phe, which corresponds to the last five amino acids of the receptor and is strictly conserved among E. coli serine amd aspartate receptors and the Salmonella typhimurium aspartate receptor, was found to have all the binding activity of the full-length receptor and the C-fragments. An in vitro methylation assay was used to obtain evidence for the physiological significance of this interaction in which excess peptide was able to completely block receptor methylation. The location of the binding site far from the methylation sites in the primary structure of the receptor suggests that the principle role of this interaction may be to hold the transferase in close proximity to all the methylation sites. Intersubunit methylation implication is proposed as plausible consequence of this "controlled proximity" mechanism since the ribose-galactose and dipeptide receptors lack the transferase binding sequence, and appear unable to bind transferase. Intersubunit methylation implies that transferase bound to eother the serine or aspartate receptor subunit may catalyze methylation of receptor subunits in a neighboring dimer, including those that have ligand specificity.
- Ogawa H
- [Glycine methyltransferase: structure, function and a variety of ligand- bindings]
- Tanpakushitsu Kakusan Koso. 1996; 41: 908-14
- West AH, Djordjevic S, Martinez-Hackert E, Stock AM
- Purification, crystallization, and preliminary X-ray diffraction analyses of the bacterial chemotaxis receptor modifying enzymes.
- Proteins. 1995; 21: 345-50
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Bacterial chemotaxis receptor modifying enzymes from Salmonella typhimurium have been crystallized using microseeding techniques. The crystals of the S-adenosyl-L-methionine-dependent methyltransferase, CheR, belong to the monoclinic space group P21 with cell constants a = 55.1 A, b = 48.1 A, c = 63.1 A, beta = 112.3 degrees. The crystals of the catalytic domain of the methylesterase, CheB, belong to the trigonal space group P3(2)21 or P3(1)21 with unit cell dimensions of a = b = 63.4 A, c = 86.8 A. Both crystals contain one molecule per asymmetric unit and have calculated Matthews' volumes of 2.4 A3/Da.
- Giner JL, Rando RR
- Novel methyltransferase activity modifying the carboxy terminal bis(geranylgeranyl)-Cys-Ala-Cys structure of small GTP-binding proteins.
- Biochemistry. 1994; 33: 15116-23
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Proteins containing CX3, CXC, and CC (where C is cysteine and X is undefined) undergo posttranslational isoprenylation at their cysteine residues. In the case of proteins which terminate in CX3, proteolytic removal of X3 is followed by the carboxymethylation of the isoprenylated cysteine residue. CXC proteins also undergo C-terminal methylation. The present study addresses the question of whether this methylation is catalyzed by a different isoprenylated protein methyltransferase than that previously described for CX3 proteins. The S-adenosylmethionine (AdoMet) dependent methylation of a small peptide-N-acetyl-S-geranylgeranyl-L-cysteinyl-L-alanyl-S-geranylgeranyl- L- cysteine (Ac(GG)CysAla(GG)Cys)--was investigated using membranes from a variety of bovine tissues as sources of enzyme. Ac(GG)CysAla(GG)Cys was a substrate for methylation, while Ac(GG)Cys(GG)Cys was not. Reciprocal inhibition studies on the methylation reactions of the CXC peptide and of N-acetyl-S-farnesyl-L-cysteine (AFC), a previously described methyltransferase substrate, suggested that these reactions are catalyzed by distinct enzymatic activities. Farnesylthioacetic acid (FTA), a potent competitive inhibitor of the methylation of AFC, did not inhibit the methylation of the CXC peptide. Moreover the KI values for S-adenosylhomocysteine and S-adenosylethionine inhibition differed for the two enzymatic activities. These data indicate that more than one AdoMet-dependent methyltransferase is involved in the carboxymethylation of isoprenylated proteins.
- Biemann HP, Koshland DE Jr
- Aspartate receptors of Escherichia coli and Salmonella typhimurium bind ligand with negative and half-of-the-sites cooperativity.
- Biochemistry. 1994; 33: 629-34
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The aspartate receptors of Escherichia coli and Salmonella typhimurium which mediate chemotactic responsiveness to aspartate have 79% amino acid sequence identity but exhibited apparently quite different aspartate binding plots. The Scatchard plot of the Salmonella receptor was concave upward whereas the E. coli receptor gave a straight line. Because the two binding sites in the Salmonella receptor lacking aspartate have a 2-fold crystallographic symmetry axis and do not overlap, the observation of more than one class of binding sites must be due to a ligand-induced conformational change giving negative cooperativity. The closely related E. coli receptor was found to bind with only one class of sites but with a stoichiometry of one aspartate per dimer. The E. coli receptor thus binds with half-of-sites reactivity, an extreme form of negative cooperativity in which the second ligand is not observed to bind at all. Comparison of the X-ray crystal structure of the ligand binding domain with and without bound aspartate revealed ligand-induced conformational changes that explain the two examples of negative cooperativity.
- Kagan RM, Clarke S
- Widespread occurrence of three sequence motifs in diverse S-adenosylmethionine-dependent methyltransferases suggests a common structure for these enzymes.
- Arch Biochem Biophys. 1994; 310: 417-27
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Three regions of sequence similarity have been reported in several protein and small-molecule S-adenosylmethionine-dependent methyltransferases. Using multiple alignments, we have now identified these three regions in a much broader group of methyltransferases and have used these data to define a consensus for each region. Of the 84 non-DNA methyltransferase sequences in the GenBank, NBRF PIR, and Swissprot databases comprising 37 distinct enzymes, we have found 69 sequences possessing motif I. This motif is similar to a conserved region previously described in DNA adenine and cytosine methyltransferases. Motif II is found in 46 sequences, while motif III is found in 61 sequences. All three regions are found in 45 of these enzymes, and an additional 15 have motifs I and III. The motifs are always found in the same order on the polypeptide chain and are separated by comparable intervals. We suggest that these conserved regions contribute to the binding of the substrate S-adenosylmethionine and/or the product S-adenosylhomocysteine. These motifs can also be identified in certain nonmethyltransferases that utilize either S-adenosylmethionine or S-adenosylhomocysteine, including S-adenosylmethionine decarboxylase, S-adenosylmethionine synthetase, and S-adenosylhomocysteine hydrolase. In the latter two types of enzymes, motif I is similar to the conserved nucleotide binding motif of protein kinases and other nucleotide binding proteins. These motifs may be of use in predicting methyltransferases and related enzymes from the open reading frames generated by genomic sequencing projects.
- Syed SK, Kim S, Paik WK
- Identification of the S-adenosyl-L-methionine binding site of protein-carboxyl O-methyltransferase using 8-azido-S-adenosyl-L-methionine.
- Biochemistry. 1993; 32: 2242-7
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Protein-carboxyl O-methyltransferase (protein methylase II) transfers the methyl group from S-adenosyl-L-methionine (AdoMet) to the carboxyl side chains of the amino acids in the proteins. We have used the radiolabeled analogue of AdoMet, 8-azido-S-adenosyl-L-[methyl-3H]methionine (8-N3-Ado[methyl-3H]Met), to investigate the AdoMet binding site of protein methylase II. The incorporation of the photoaffinity label in the enzyme upon UV irradiation is highly specific. In the absence of UV irradiation or if the photoprobe is irradiated prior to its addition to the reaction mixture, no photoinsertion of the label occurs. Moreover, the presence of a competitive inhibitor of protein methylase II, S-adenosyl-L-homocysteine (AdoHcy), or the unlabeled AdoMet itself in the reaction mixture diminished labeling of the enzyme. Sequential digestion of the labeled enzyme with trypsin, chymotrypsin, and endoproteinase Glu-C yielded a modified and radiolabeled decapeptide. When compared with the reported primary amino acid sequence of protein methylase II from rat brain, the amino acid composition of the decapeptide matched residues 113-121. This segment forms the midpoint region of the enzyme (234 amino acid residues). An important characteristic of the sequence is the presence of two adjacent aspartic acid residues (Asp117-Asp118) which most likely provide the negative charge environment for the sulfonium moiety of the AdoMet molecule.
- Borczuk A, Stock A, Stock J
- S-adenosylmethionine may not be essential for signal transduction during bacterial chemotaxis.
- J Bacteriol. 1987; 169: 3295-300
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We previously showed that a mutant strain of Salmonella typhimurium completely deficient in both the chemoreceptor methylating (CheR) and demethylating (CheB) enzymes can still exhibit chemotaxis to aspartate and other attractants (J. Stock, A. Borczuk, F. Chiou, and J. E. B. Burchenal, Proc. Natl. Acad. Sci. USA 82:8364-8368, 1985). We used this cheR cheB mutant to examine the possibility of an additional requirement for S-adenosylmethionine in chemotaxis besides its role in chemoreceptor methylation. A metE mutation was transduced into a cheR cheB double mutant, and the cells were starved for methionine. Despite the fact that intracellular S-adenosylmethionine dropped from approximately 100 microM to less than 0.2 microM, chemotaxis was largely unaffected. In contrast, a corresponding cheR+ cheB+ metE mutant completely lost its chemotaxis ability after being starved for methionine. We conclude from this observation that the primary requirement for S-adenosylmethionine during bacterial chemotaxis is in the methylation of receptor proteins.
- Van Der Werf P, Koshland DE Jr
- Identification of a gamma-glutamyl methyl ester in bacterial membrane protein involved in chemotaxis.
- J Biol Chem. 1977; 252: 2793-5
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Evidence is presented that a methyltransferase enzyme, previously shown to be necessary for chemotaxis and identified as the cheR gene product, catalyzes the formation of a gamma-glutamyl methyl ester in one or more membrane proteins of Salmonella typhimurium. The rates of release of methyl label from the methylated protein in acid, base, and hydroxylamine are consistent with a methyl ester and not with a methylated imidazole, guanidino, or amino group. A gamma-glutamyl methyl ester was isolated from a proteolytic digest of the modified protein.
- Kim S, Paik WK
- Labile protein-methyl ester: comparison between chemically and enzymatically synthesized.
- Experientia. 1976; 32: 982-4
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The rate of hydrolysis of protein-methyl ester, the enzymatic product of S-adenosylmethionine: protein-carboxyl methyltransferase (EC.2.1.1.24) acting on oxidized ribonuclease, was measured at pH 7.1 and 8.6 at 37 degrees C. The half-life of the hydrolysis of the ester is 25 min at pH 7.1, and 4 min at 8.6. The rate of hydrolysis of the enzymatically formed esters at pH 7.0, in 0.1 M phosphate buffer, was about 25 times faster than that of esters formed chemically by reaction with methanol in HCl. The lability of the enzymatically synthesized protein-methyl ester suggests that the esterification is specific to sites such that ionization of neighboring amino acid side chains enhances the rate of the hydrolysis.