Secondary literature sources for CENPB
The following references were automatically generated.
- Fujii Y, Shimizu T, Kusumoto M, Kyogoku Y, Taniguchi T, Hakoshima T
- Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences.
- EMBO J. 1999; 18: 5028-41
- Display abstract
There has been growing interest in the role of the IRF (interferon regulatory factor) family of transcription factors in the regulation of immune responses, cytokine signaling, and oncogenesis. These members are characterized by their well-conserved DNA binding domains at the N-terminal regions. Here we report the 2.2 A resolution crystal structure of the DNA binding domain of one such family member, IRF-2, bound to DNA. The structure reveals its recognition sequence, AANNGAAA (here, recognized bases are underlined and in bold, and N indicates any base), and its cooperative binding to a tandem repeat of the GAAA core sequence induced by DNA structure distortions. These facts explain well the diverse binding properties of the IRF family members, which bind to both single and tandemly repeated sequences. Furthermore, we also identified the 'helix-hairpin-strand motif' at the C terminus of the recognition helix as a metal binding site that is commonly found in certain classes of DNA-interactive proteins. Our results provide new insights into the structure and function of this family of transcription factors.
- Sunnerhagen M, Nilges M, Otting G, Carey J
- Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA.
- Nat Struct Biol. 1997; 4: 819-26
- Display abstract
The structure of the monomeric DNA-binding domain of the Escherichia coli arginine repressor, ArgR, determined by NMR spectroscopy, shows structural homology to the winged helix-turn-helix (wHTH) family, a motif found in a diverse class of proteins including both gene regulators and gene organizers from prokaryotes and eukaryotes. Biochemical data on DNA binding by intact ArgR are used as constraints to position the domain on its DNA target and to derive a model for the hexamer-DNA complex using the known structure of the L-arginine-binding domain. The structural independence of the wHTH fold may be important for multimeric DNA-binding proteins that contact extended DNA regions with imperfect match to consensus sequences, a feature of many wHTH-domain proteins.
- Suck D
- Common fold, common function, common origin?
- Nat Struct Biol. 1997; 4: 161-5
- Toth M, Grimsby J, Buzsaki G, Donovan GP
- Epileptic seizures caused by inactivation of a novel gene, jerky, related to centromere binding protein-B in transgenic mice.
- Nat Genet. 1995; 11: 71-5
- Display abstract
Epidemiological data and genetic studies indicate that certain forms of human epilepsy are inherited. Based on the similarity between the human and mouse genomes, mouse models of epilepsy could facilitate the discovery of genes associated with epilepsy syndromes. Here, we report an insertional murine mutation that inactivates a novel gene and results in whole body jerks, generalized clonic seizures, and epileptic brain activity in transgenic mice. The gene, named jerky, encodes a putative 41.7 kD protein displaying homology to a number of nuclear regulatory proteins, suggesting that perhaps the jerky protein is able to bind DNA.
- Lam E
- Domain analysis of the plant DNA-binding protein GT1a: requirement of four putative alpha-helices for DNA binding and identification of a novel oligomerization region.
- Mol Cell Biol. 1995; 15: 1014-20
- Display abstract
Light is an important environmental signal that can influence diverse developmental processes in plants. Many plant nuclear genes respond to light at the level of transcription initiation. GT-1 and GT2 are nuclear factors which interact with DNA sequences in many light-responsive gene promoters. cDNA clones which encode proteins with sequence binding specificities similar to those of these two factors have been isolated. They show significant amino acid sequence similarities within three closely spaced, putative alpha-helices that were predicted by secondary structure analysis but do not show significant homologies with any other reported DNA-binding protein. In this work, N- and C-terminal deletions of tobacco GT1a were generated by in vitro transcription and translation, and their DNA-binding activities and subunit structures were studied. The results suggest that the C-terminal domain of GT1a is critical for protein oligomerization, while a region predicted to contain four closely spaced alpha-helices is required for DNA binding. Direct chemical cross-linking and gel filtration analyses of full-length and truncated derivatives of GT1a suggest that this factor can exist in solution as a homotetramer and that oligomerization is independent of DNA binding. This study thus establishes two independent functional domains in this class of eukaryotic trans-acting factors. Possible implications of the multimeric nature of GT1a in relation to the known characteristics of light-responsive promoter architecture are discussed.
- Haaf T, Ward DC
- Rabl orientation of CENP-B box sequences in Tupaia belangeri fibroblasts.
- Cytogenet Cell Genet. 1995; 70: 258-62
- Display abstract
The chromosomes of the tree shrew Tupaia belangeri exhibit highly localized CENP-B box sequences in the centromeric regions of most chromosomes. Telomeric sequences are present at the ends of all chromosomes and, in addition, at specific interstitial chromosomal sites that likely represent remnants of ancestral telomeres. This suggests that Robertsonian and tandem chromosome fusion events have occurred in the karyotypic evolution of Tupaiidae. In Tupaia skin fibroblasts CENP-B boxes are almost always clustered together at one pole of the interphase nucleus, whereas the telomeric domains are relatively evenly distributed throughout the whole nuclear volume. The observed orientation of the centromeres is reminiscent of the Rabl polarization of chromosomes; this is the first mammalian cell substrate in which such an higher-order chromosomal organization has been observed. CENP-B box sequences are found in several other mammalian species. The implications for recent parallel evolution of CENP-B binding motifs and concerted evolution of these sequences are discussed.
- Yang W, Steitz TA
- Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.
- Cell. 1995; 82: 193-207
- Display abstract
The structure of gamma delta resolvase complexed with a 34 bp substrate DNA has been determined at 3.0 A resolution. The DNA is sharply bent by 60 degrees toward the major groove and away from the resolvase catalytic domains at the recombination crossover point. The C-terminal one third of resolvase, which was disordered in the absence of DNA, forms an arm and a 3-helix DNA-binding domain on the opposite side of the DNA from the N-terminal domain. The arms wrap around the minor groove of the central 16 bp, and the DNA-binding domains interact with the major grooves near the outer boundaries of the binding site. The resolvase dimer is asymmetric, particularly in the arm region, implying a conformational adaptability that may be important for resolvase binding to different DNA sites in the synaptosome. It also raises the possibility of a sequential single-strand cleavage mechanism.
- Phillips SE
- Built by association: structure and function of helix-loop-helix DNA-binding proteins.
- Structure. 1994; 2: 1-4
- Sugimoto K, Furukawa K, Himeno M
- Functional cloning of centromere protein B (CENP-B) box-enriched alphoid DNA repeats utilizing the sequence-specific DNA binding activity of human CENP-B in vitro.
- Chromosome Res. 1994; 2: 453-9
- Display abstract
The centromere is a distinctive portion of the chromosome consisting of 'centromere DNA' and 'centromere proteins'. Recently, a direct molecular interaction was discovered between human centromere protein B (CENP-B) and human centromeric alphoid repeats. This enabled us to isolate the CENP-B-targeted centromeric DNA sequences by positively utilizing the biologic activity of CENP-B in vitro. In the previous model experiment, we found that oligonucleotides covering the CENP-B binding sequences were enriched by the DNA immunoprecipitation procedure. Here we apply the same technique to the direct isolation of a functional part of human centromeric DNA from a genomic DNA library. Restriction digestion of two isolated clones showed the typical repeating pattern of an alphoid family that is known to localize at the centromeric region of all human chromosomes. Sequence analysis showed that these two clones frequently contain the authentic CENP-B binding motif, CTTCGTTGGAAACGGGA, or a new one with one base replaced, CTTCGTTGGAAACGGGT. The frequent distribution of these motifs suggests that the isolated sequences are directly involved in the organization of centromeric heterochromatin at the primary constriction in conjunction with CENP-B.
- Freire R, Salas M, Hermoso JM
- A new protein domain for binding to DNA through the minor groove.
- EMBO J. 1994; 13: 4353-60
- Display abstract
Protein p6 of the Bacillus subtilis phage phi 29 binds with low sequence specificity to DNA through the minor groove, forming a multimeric nucleoprotein complex that activates the initiation of phi 29 DNA replication. Deletion analysis suggested that the N-terminal part of protein p6, predicted to form an amphipathic alpha-helix, is involved in DNA binding. We have constructed site-directed mutants at the polar side of the putative alpha-helix. DNA binding and activation of initiation of phi 29 DNA replication were impaired in most of the mutant proteins obtained. A 19 amino acid peptide comprising the N-terminus of protein p6 interacted with a DNA fragment containing high-affinity signals for protein p6 binding with approximately 50-fold higher affinity than the peptide corresponding to an inactive mutant. Both wild-type peptide and protein p6 recognized the same sequences in this DNA fragment. This result, together with distamycin competition experiments, suggested that the wild-type peptide also binds to DNA through the minor groove. In addition, CD spectra of the wild-type peptide showed an increase in the alpha-helical content when bound to DNA. All these results indicate that an alpha-helical structure located in the N-terminal region of protein p6 is involved in DNA binding through the minor groove.
- Ogata K et al.
- Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices.
- Cell. 1994; 79: 639-48
- Display abstract
The DNA-binding region of Myb consists of three imperfect tandem repeats (R1, R2, and R3). We have determined the solution structure of a specific DNA complex of the minimum DNA-binding domain (R2R3) by heteronuclear multidimensional NMR. Both R2 and R3 contain three helices, and the third helix in each is found to be a recognition helix. R2 and R3 are closely packed in the major groove, so that the two recognition helices contact each other directly to bind to the specific base sequence, AACNG cooperatively; this is a significant arrangement of recognition helices. The three key base pairs in this sequence are specifically recognized by Asn-183 (R3), Lys-182 (R3), and Lys-128 (R2). In contrast, R1 has no specific interactions with DNA from our NMR study of the DNA complex of the full DNA-binding domain (R1R2R3).
- Kornberg TB
- Understanding the homeodomain.
- J Biol Chem. 1993; 268: 26813-6
- Landsman D, Bustin M
- A signature for the HMG-1 box DNA-binding proteins.
- Bioessays. 1993; 15: 539-46
- Display abstract
A diverse group of DNA-binding regulatory proteins share a common structural domain which is homologous to the sequence of a highly conserved and abundant chromosomal protein, HMG-1. Proteins containing this HMG-1 box regulate various cellular functions involving DNA binding, suggesting that the target DNA sequences share a common structural element. Members of this protein family exhibit a dual DNA-binding specificity: each recognizes a unique sequence as well as a common DNA conformation. The highly conserved HMG-1/-2 proteins may modulate the binding of other HMG-1 box proteins to bent DNA. We examine the structural and functional relationships between the proteins, identify their signature and describe common features of their target DNA elements.
- Yoda K, Kitagawa K, Masumoto H, Muro Y, Okazaki T
- A human centromere protein, CENP-B, has a DNA binding domain containing four potential alpha helices at the NH2 terminus, which is separable from dimerizing activity.
- J Cell Biol. 1992; 119: 1413-27
- Display abstract
The alphoid DNA-CENP-B (centromere protein B) complex is the first sequence-specific DNA/protein complex detected in the centromeric region of human chromosomes. In the reaction, CENP-B recognizes a 17-bp sequence (CENP-B box) and assembles two alphoid DNA molecules into a complex, which is designated complex A (Muro, Y., H. Masumoto, K. Yoda, N. Nozaki, M. Ohashi, and T. Okazaki. 1992. J. Cell Biol. 116:585-596). Since CENP-B gene is conserved in mammalian species and CENP-B boxes are found also in mouse centromere satellite DNA (minor satellite), this sequence-specific DNA-protein interaction may be important for some kind of common centromere function. In this study we have characterized the structure of CENP-B and CENP-B-alphoid DNA complex. We have shown by chemical cross-linking that CENP-B formed a dimer, and have estimated by molecular weight determination the composition of complex A to be a CENP-B dimer and two molecules of alphoid DNA. The DNA binding domain has been delimited within the NH2-terminal 125-amino acid region containing four potential alpha-helices using truncated CENP-B made in Escherichia coli cells. We have shown that CENP-B had sites highly sensitive to proteases and that the DNA binding domain was separable from the dimerizing activity by the proteolytic cleavage at 20 kD from the COOH terminus of the molecule. Thus, CENP-B may organize a higher order structure in the centromere by juxtaposing two CENP-B boxes in the alphoid DNA repeat through both the DNA-protein and protein-protein interactions.
- Sugimoto K, Muro Y, Himeno M
- Anti-helix-loop-helix domain antibodies: discovery of autoantibodies that inhibit DNA binding activity of human centromere protein B (CENP-B).
- J Biochem (Tokyo). 1992; 111: 478-83
- Display abstract
Centromere protein B (CENP-B) is one of the centromere DNA binding proteins constituting centromeric heterochromatin of human chromosomes. This protein was originally identified as the target antigen in autoimmune disease patients (often with scleroderma). In this study, we cloned a human CENP-B cDNA which was longer than the previously isolated one and expressed functional recombinant CENP-B in Escherichia coli. The DNA binding domain was finely located within the N-terminal 134-amino-acid residues covering a predicted helix-loop-helix (HLH) structure, by using a set of recombinant products with stepwise deletions from the C-terminus. From the analysis of their reactivity to anti-centromere sera from autoimmune disease patients, four epitopes were mapped on CENP-B antigen. In addition to two epitopes at the C-terminus, two were found on the HLH region at the N-terminus. In the analysis of the interaction between the antigen and autoantibodies, we found that the DNA binding activity of CENP-B was distorted by the attack of the anti-HLH domain antibodies in in vitro binding reactions. Our results suggest that the direct inhibition of the DNA binding activity by the autoantibodies might be involved in patients' autoimmune reactions in vivo.
- Sugimoto K, Wakisaka E, Himeno M
- Cycled DNA immunoprecipitation procedure to enrich the target sequences for DNA binding proteins with the fold purification monitored.
- Anal Biochem. 1992; 207: 114-20
- Display abstract
Using centromere DNA binding protein (CENP-B) expressed as a fusion to beta-galactosidase in Escherichia coli, we established a cycled DNA immunoprecipitation procedure for enriching CENP-B binding sequences and monitoring the enrichment process. Degenerated synthetic oligonucleotides for an authentic CENP-B binding sequence, inserted into a pUC-derived vector, were incubated with the crude CENP-B extract. DNA-protein complexes formed in vitro were immunologically precipitated utilizing the beta-galactosidase moiety as a tagged antigen. The effectiveness of repeating cycles of immunoprecipitation was demonstrated by the color selection method designed for pUC-derived plasmids, after introducing the precipitated plasmids into Escherichia coli. After three cycles of DNA immunoprecipitation, only a few kinds of sequences constituted the majority. By repeating two more cycles, the most predominant sequence was finally enriched until homogeneous, indicating the enrichment of the binding sequences in a hierarchical order. Further application to human genomic DNA showed that two EcoRI DNA fragments, 0.49 and 0.78 kb in size, were exclusively identified. This procedure can be applied to the systematic analysis of binding sequences for any other DNA binding proteins without production of any specific antibodies or further purification.
- Pluta AF, Saitoh N, Goldberg I, Earnshaw WC
- Identification of a subdomain of CENP-B that is necessary and sufficient for localization to the human centromere.
- J Cell Biol. 1992; 116: 1081-93
- Display abstract
We have combined in vivo and in vitro approaches to investigate the function of CENP-B, a major protein of human centromeric heterochromatin. Expression of epitope-tagged deletion derivatives of CENP-B in HeLa cells revealed that a single domain less than 158 residues from the amino terminus of the protein is sufficient to localize CENP-B to centromeres. Centromere localization was abolished if as few as 28 amino acids were removed from the amino terminus of CENP-B. The centromere localization signal of CENP-B can function in an autonomous fashion, relocating a fused bacterial enzyme to centromeres. The centromere localization domain of CENP-B specifically binds in vitro to a subset of alpha-satellite DNA monomers. These results suggest that the primary mechanism for localization of CENP-B to centromeres involves the recognition of a DNA sequence found at centromeres. Analysis of the distribution of this sequence in alpha-satellite DNA suggests that CENP-B binding may have profound effects on chromatin structure at centromeres.
- Reidhaar-Olson JF et al.
- Random mutagenesis of protein sequences using oligonucleotide cassettes.
- Methods Enzymol. 1991; 208: 564-86
- Affolter M et al.
- Similarities between the homeodomain and the Hin recombinase DNA-binding domain.
- Cell. 1991; 64: 879-80
- Dervan PB
- Characterization of protein-DNA complexes by affinity cleaving.
- Methods Enzymol. 1991; 208: 497-515
- Laughon A
- DNA binding specificity of homeodomains.
- Biochemistry. 1991; 30: 11357-67
- Wistow G
- Cold shock and DNA binding.
- Nature. 1990; 344: 823-4
- Travers AA
- DNA conformation and protein binding.
- Annu Rev Biochem. 1989; 58: 427-52
- Kano Y
- [Structure and function of HU protein]
- Tanpakushitsu Kakusan Koso. 1988; 33: 239-51
