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Nucleic Acids Res. Jul 25, 1995; 23(14): 2685–2691.
PMCID: PMC307093

A variety of DNA-binding and multimeric proteins contain the histone fold motif.

Abstract

The histone fold motif has previously been identified as a structural feature common to all four core histones and is involved in both histone-histone and histone-DNA interactions. Through the use of a novel motif searching method, a group of proteins containing the histone fold motif has been established. The proteins in this group are involved in a wide variety of functions related mostly to DNA metabolism. Most of these proteins engage in protein-protein or protein-DNA interactions, as do their core histone counterparts. Among these, CCAAT-specific transcription factor CBF and its yeast homologue HAP are two examples of multimeric complexes with different component subunits that contain the histone fold motif. The histone fold proteins are distantly related, with a relatively small degree of absolute sequence similarity. It is proposed that these proteins may share a similar three-dimensional conformation despite the lack of significant sequence similarity.

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  • Kornberg RD, Thomas JO. Chromatin structure; oligomers of the histones. Science. 1974 May 24;184(4139):865–868. [PubMed]
  • DeLange RJ, Fambrough DM, Smith EL, Bonner J. Calf and pea histone IV. 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone. J Biol Chem. 1969 Oct 25;244(20):5669–5679. [PubMed]
  • Eickbush TH, Moudrianakis EN. The histone core complex: an octamer assembled by two sets of protein-protein interactions. Biochemistry. 1978 Nov 14;17(23):4955–4964. [PubMed]
  • Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN. The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10148–10152. [PMC free article] [PubMed]
  • Arents G, Moudrianakis EN. Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA. Proc Natl Acad Sci U S A. 1993 Nov 15;90(22):10489–10493. [PMC free article] [PubMed]
  • Kokubo T, Gong DW, Wootton JC, Horikoshi M, Roeder RG, Nakatani Y. Molecular cloning of Drosophila TFIID subunits. Nature. 1994 Feb 3;367(6462):484–487. [PubMed]
  • Pehrson JR, Fried VA. MacroH2A, a core histone containing a large nonhistone region. Science. 1992 Sep 4;257(5075):1398–1400. [PubMed]
  • Bairoch A, Boeckmann B. The SWISS-PROT protein sequence data bank, recent developments. Nucleic Acids Res. 1993 Jul 1;21(13):3093–3096. [PMC free article] [PubMed]
  • Barker WC, George DG, Mewes HW, Pfeiffer F, Tsugita A. The PIR-International databases. Nucleic Acids Res. 1993 Jul 1;21(13):3089–3092. [PMC free article] [PubMed]
  • Benson D, Lipman DJ, Ostell J. GenBank. Nucleic Acids Res. 1993 Jul 1;21(13):2963–2965. [PMC free article] [PubMed]
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. [PubMed]
  • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. [PMC free article] [PubMed]
  • Tatusov RL, Altschul SF, Koonin EV. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12091–12095. [PMC free article] [PubMed]
  • Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A. 1990 Mar;87(6):2264–2268. [PMC free article] [PubMed]
  • Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol. 1993 Jul 20;232(2):584–599. [PubMed]
  • Rost B, Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins. 1994 May;19(1):55–72. [PubMed]
  • Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986 Apr;5(4):823–826. [PMC free article] [PubMed]
  • Chothia C. Proteins. One thousand families for the molecular biologist. Nature. 1992 Jun 18;357(6379):543–544. [PubMed]
  • Kruger W, Herskowitz I. A negative regulator of HO transcription, SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1. Mol Cell Biol. 1991 Aug;11(8):4135–4146. [PMC free article] [PubMed]
  • Baxevanis AD, Bryant SH, Landsman D. Homology model building of the HMG-1 box structural domain. Nucleic Acids Res. 1995 Mar 25;23(6):1019–1029. [PMC free article] [PubMed]
  • Tabassum R, Sandman KM, Reeve JN. HMt, a histone-related protein from Methanobacterium thermoautotrophicum delta H. J Bacteriol. 1992 Dec;174(24):7890–7895. [PMC free article] [PubMed]
  • Sandman K, Krzycki JA, Dobrinski B, Lurz R, Reeve JN. HMf, a DNA-binding protein isolated from the hyperthermophilic archaeon Methanothermus fervidus, is most closely related to histones. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5788–5791. [PMC free article] [PubMed]
  • Agha-Amiri K, Klein A. Nucleotide sequence of a gene encoding a histone-like protein in the archaeon Methanococcus voltae. Nucleic Acids Res. 1993 Mar 25;21(6):1491–1491. [PMC free article] [PubMed]
  • Vuorio T, Maity SN, de Crombrugghe B. Purification and molecular cloning of the "A" chain of a rat heteromeric CCAAT-binding protein. Sequence identity with the yeast HAP3 transcription factor. J Biol Chem. 1990 Dec 25;265(36):22480–22486. [PubMed]
  • Sinha S, Maity SN, Lu J, de Crombrugghe B. Recombinant rat CBF-C, the third subunit of CBF/NFY, allows formation of a protein-DNA complex with CBF-A and CBF-B and with yeast HAP2 and HAP3. Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1624–1628. [PMC free article] [PubMed]
  • Xing Y, Fikes JD, Guarente L. Mutations in yeast HAP2/HAP3 define a hybrid CCAAT box binding domain. EMBO J. 1993 Dec;12(12):4647–4655. [PMC free article] [PubMed]
  • Hahn S, Pinkham J, Wei R, Miller R, Guarente L. The HAP3 regulatory locus of Saccharomyces cerevisiae encodes divergent overlapping transcripts. Mol Cell Biol. 1988 Feb;8(2):655–663. [PMC free article] [PubMed]
  • Olesen J, Hahn S, Guarente L. Yeast HAP2 and HAP3 activators both bind to the CYC1 upstream activation site, UAS2, in an interdependent manner. Cell. 1987 Dec 24;51(6):953–961. [PubMed]
  • Weinzierl RO, Ruppert S, Dynlacht BD, Tanese N, Tjian R. Cloning and expression of Drosophila TAFII60 and human TAFII70 reveal conserved interactions with other subunits of TFIID. EMBO J. 1993 Dec 15;12(13):5303–5309. [PMC free article] [PubMed]
  • Ha I, Lane WS, Reinberg D. Cloning of a human gene encoding the general transcription initiation factor IIB. Nature. 1991 Aug 22;352(6337):689–695. [PubMed]
  • Pisani FM, De Martino C, Rossi M. A DNA polymerase from the archaeon Sulfolobus solfataricus shows sequence similarity to family B DNA polymerases. Nucleic Acids Res. 1992 Jun 11;20(11):2711–2716. [PMC free article] [PubMed]
  • Stout V, Gottesman S. RcsB and RcsC: a two-component regulator of capsule synthesis in Escherichia coli. J Bacteriol. 1990 Feb;172(2):659–669. [PMC free article] [PubMed]
  • Jin S, Ishimoto K, Lory S. Nucleotide sequence of the rpoN gene and characterization of two downstream open reading frames in Pseudomonas aeruginosa. J Bacteriol. 1994 Mar;176(5):1316–1322. [PMC free article] [PubMed]
  • Simon MA, Bowtell DD, Dodson GS, Laverty TR, Rubin GM. Ras1 and a putative guanine nucleotide exchange factor perform crucial steps in signaling by the sevenless protein tyrosine kinase. Cell. 1991 Nov 15;67(4):701–716. [PubMed]
  • Inostroza JA, Mermelstein FH, Ha I, Lane WS, Reinberg D. Dr1, a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. Cell. 1992 Aug 7;70(3):477–489. [PubMed]
  • Kaul R, Gray GJ, Koehncke NR, Gu LJ. Cloning and sequence analysis of the Chlamydia trachomatis spc ribosomal protein gene cluster. J Bacteriol. 1992 Feb;174(4):1205–1212. [PMC free article] [PubMed]
  • Zinoni F, Birkmann A, Stadtman TC, Böck A. Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli. Proc Natl Acad Sci U S A. 1986 Jul;83(13):4650–4654. [PMC free article] [PubMed]
  • Blattner FR, Burland V, Plunkett G, 3rd, Sofia HJ, Daniels DL. Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov 25;21(23):5408–5417. [PMC free article] [PubMed]
  • Axley MJ, Grahame DA, Stadtman TC. Escherichia coli formate-hydrogen lyase. Purification and properties of the selenium-dependent formate dehydrogenase component. J Biol Chem. 1990 Oct 25;265(30):18213–18218. [PubMed]
  • de Lorimier R, Guglielmi G, Bryant DA, Stevens SE., Jr Structure and mutation of a gene encoding a Mr 33,000 phycocyanin-associated linker polypeptide. Arch Microbiol. 1990;153(6):541–549. [PubMed]
  • Serghini MA, Fuchs M, Pinck M, Reinbolt J, Walter B, Pinck L. RNA2 of grapevine fanleaf virus: sequence analysis and coat protein cistron location. J Gen Virol. 1990 Jul;71(Pt 7):1433–1441. [PubMed]
  • Josephs SF, Ablashi DV, Salahuddin SZ, Jagodzinski LL, Wong-Staal F, Gallo RC. Identification of the human herpesvirus 6 glycoprotein H and putative large tegument protein genes. J Virol. 1991 Oct;65(10):5597–5604. [PMC free article] [PubMed]
  • Ludevid D, Höfte H, Himelblau E, Chrispeels MJ. The Expression Pattern of the Tonoplast Intrinsic Protein gamma-TIP in Arabidopsis thaliana Is Correlated with Cell Enlargement. Plant Physiol. 1992 Dec;100(4):1633–1639. [PMC free article] [PubMed]
  • Shagan T, Bar-Zvi D. Nucleotide sequence of an Arabidopsis thaliana turgor-responsive cDNA clone encoding TMP-A, a transmembrane protein containing the major intrinsic protein motif. Plant Physiol. 1993 Apr;101(4):1397–1398. [PMC free article] [PubMed]
  • Kinoshita T, Hara-Nishimura I, Siraishi H, Okada K, Shimura Y, Nishimura M. Nucleotide sequence of a transmembrane protein (TMP-C) cDNA in Arabidopsis thaliana. Plant Physiol. 1994 Aug;105(4):1441–1442. [PMC free article] [PubMed]
  • Wistow G, Piatigorsky J. Recruitment of enzymes as lens structural proteins. Science. 1987 Jun 19;236(4808):1554–1556. [PubMed]
  • Wistow GJ, Lietman T, Williams LA, Stapel SO, de Jong WW, Horwitz J, Piatigorsky J. Tau-crystallin/alpha-enolase: one gene encodes both an enzyme and a lens structural protein. J Cell Biol. 1988 Dec;107(6 Pt 2):2729–2736. [PMC free article] [PubMed]
  • Bryant SH, Lawrence CE. An empirical energy function for threading protein sequence through the folding motif. Proteins. 1993 May;16(1):92–112. [PubMed]
  • Barton GJ. ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 1993 Jan;6(1):37–40. [PubMed]
  • Li XY, Hooft van Huijsduijnen R, Mantovani R, Benoist C, Mathis D. Intron-exon organization of the NF-Y genes. Tissue-specific splicing modifies an activation domain. J Biol Chem. 1992 May 5;267(13):8984–8990. [PubMed]
  • Li XY, Mantovani R, Hooft van Huijsduijnen R, Andre I, Benoist C, Mathis D. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res. 1992 Mar 11;20(5):1087–1091. [PMC free article] [PubMed]
  • Hooft van Huijsduijnen R, Li XY, Black D, Matthes H, Benoist C, Mathis D. Co-evolution from yeast to mouse: cDNA cloning of the two NF-Y (CP-1/CBF) subunits. EMBO J. 1990 Oct;9(10):3119–3127. [PMC free article] [PubMed]
  • Keller JW, Baurick KB, Rutt GC, O'Malley MV, Sonafrank NL, Reynolds RA, Ebbesson LO, Vajdos FF. Pseudomonas cepacia 2,2-dialkylglycine decarboxylase. Sequence and expression in Escherichia coli of structural and repressor genes. J Biol Chem. 1990 Apr 5;265(10):5531–5539. [PubMed]
  • Prangishvili D, Klenk HP. Nucleotide sequence of the gene for a 74 kDa DNA polymerase from the archaeon Sulfolobus solfataricus. Nucleic Acids Res. 1993 Jun 11;21(11):2768–2768. [PMC free article] [PubMed]
  • Van Dyck L, Pearce DA, Sherman F. PIM1 encodes a mitochondrial ATP-dependent protease that is required for mitochondrial function in the yeast Saccharomyces cerevisiae. J Biol Chem. 1994 Jan 7;269(1):238–242. [PubMed]
  • McNabb DS, Xing Y, Guarente L. Cloning of yeast HAP5: a novel subunit of a heterotrimeric complex required for CCAAT binding. Genes Dev. 1995 Jan 1;9(1):47–58. [PubMed]
  • Purnelle B, Coster F, Goffeau A. The sequence of a 36 kb segment on the left arm of yeast chromosome X identifies 24 open reading frames including NUC1, PRP21 (SPP91), CDC6, CRY2, the gene for S24, a homologue to the aconitase gene ACO1 and two homologues to chromosome III genes. Yeast. 1994 Sep;10(9):1235–1249. [PubMed]
  • Dodd HM, Bennett PM. The R46 site-specific recombination system is a homologue of the Tn3 and gamma delta (Tn1000) cointegrate resolution system. J Gen Microbiol. 1987 Aug;133(8):2031–2039. [PubMed]
  • Assinder SJ, de Marco P, Sayers JR, Shaw LE, Winson MK, Williams PA. Identical resolvases are encoded by Pseudomonas TOL plasmids pWW53 and pDK1. Nucleic Acids Res. 1992 Oct 25;20(20):5476–5476. [PMC free article] [PubMed]
  • Merrick M, Gibbins J, Toukdarian A. The nucleotide sequence of the sigma factor gene ntrA (rpoN) of Azotobacter vinelandii: analysis of conserved sequences in NtrA proteins. Mol Gen Genet. 1987 Dec;210(2):323–330. [PubMed]
  • Merrick MJ, Coppard JR. Mutations in genes downstream of the rpoN gene (encoding sigma 54) of Klebsiella pneumoniae affect expression from sigma 54-dependent promoters. Mol Microbiol. 1989 Dec;3(12):1765–1775. [PubMed]
  • Köhler T, Cayrol JM, Ramos JL, Harayama S. Nucleotide and deduced amino acid sequence of the RpoN sigma-factor of Pseudomonas putida. Nucleic Acids Res. 1989 Dec 11;17(23):10125–10125. [PMC free article] [PubMed]
  • Inouye S, Yamada M, Nakazawa A, Nakazawa T. Cloning and sequence analysis of the ntrA (rpoN) gene of Pseudomonas putida. Gene. 1989 Dec 21;85(1):145–152. [PubMed]
  • Bonfini L, Karlovich CA, Dasgupta C, Banerjee U. The Son of sevenless gene product: a putative activator of Ras. Science. 1992 Jan 31;255(5044):603–606. [PubMed]
  • Chardin P, Camonis JH, Gale NW, van Aelst L, Schlessinger J, Wigler MH, Bar-Sagi D. Human Sos1: a guanine nucleotide exchange factor for Ras that binds to GRB2. Science. 1993 May 28;260(5112):1338–1343. [PubMed]
  • Bowtell D, Fu P, Simon M, Senior P. Identification of murine homologues of the Drosophila son of sevenless gene: potential activators of ras. Proc Natl Acad Sci U S A. 1992 Jul 15;89(14):6511–6515. [PMC free article] [PubMed]
  • Goodrich JA, Hoey T, Thut CJ, Admon A, Tjian R. Drosophila TAFII40 interacts with both a VP16 activation domain and the basal transcription factor TFIIB. Cell. 1993 Nov 5;75(3):519–530. [PubMed]
  • Malik S, Hisatake K, Sumimoto H, Horikoshi M, Roeder RG. Sequence of general transcription factor TFIIB and relationships to other initiation factors. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9553–9557. [PMC free article] [PubMed]
  • Tsuboi A, Conger K, Garrett KP, Conaway RC, Conaway JW, Arai N. RNA polymerase II initiation factor alpha from rat liver is almost identical to human TFIIB. Nucleic Acids Res. 1992 Jun 25;20(12):3250–3250. [PMC free article] [PubMed]
  • Hisatake K, Malik S, Roeder RG, Horikoshi M. Conserved structural motifs between Xenopus and human TFIIB. Nucleic Acids Res. 1991 Dec 11;19(23):6639–6639. [PMC free article] [PubMed]
  • Heffron F, McCarthy BJ, Ohtsubo H, Ohtsubo E. DNA sequence analysis of the transposon Tn3: three genes and three sites involved in transposition of Tn3. Cell. 1979 Dec;18(4):1153–1163. [PubMed]
  • Mabilat C, Lourençao-Vital J, Goussard S, Courvalin P. A new example of physical linkage between Tn1 and Tn21: the antibiotic multiple-resistance region of plasmid pCFF04 encoding extended-spectrum beta-lactamase TEM-3. Mol Gen Genet. 1992 Oct;235(1):113–121. [PubMed]
  • Tolmasky ME. Sequencing and expression of aadA, bla, and tnpR from the multiresistance transposon Tn1331. Plasmid. 1990 Nov;24(3):218–226. [PubMed]
  • Nobuta K, Tolmasky ME, Crosa LM, Crosa JH. Sequencing and expression of the 6'-N-acetyltransferase gene of transposon Tn1331 from Klebsiella pneumoniae. J Bacteriol. 1988 Aug;170(8):3769–3773. [PMC free article] [PubMed]
  • Purnelle B, Tettelin H, Van Dyck L, Skala J, Goffeau A. The sequence of a 17.5 kb DNA fragment on the left arm of yeast chromosome XI identifies the protein kinase gene ELM1, the DNA primase gene PRI2, a new gene encoding a putative histone and seven new open reading frames. Yeast. 1993 Dec;9(12):1379–1384. [PubMed]
  • Wilson R, Ainscough R, Anderson K, Baynes C, Berks M, Bonfield J, Burton J, Connell M, Copsey T, Cooper J, et al. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature. 1994 Mar 3;368(6466):32–38. [PubMed]
  • Sanger F, Coulson AR, Hong GF, Hill DF, Petersen GB. Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol. 1982 Dec 25;162(4):729–773. [PubMed]

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