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Nucleic Acids Res. Jun 15, 1997; 25(12): 2464–2469.
PMCID: PMC146766

Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins.


The PROSITE pattern Zinc_Finger_C2H2 was extended to permit the detection of all C2H2 zinc fingers and their parent proteins in the recently completed sequence of the yeast genome. Additionally, a new computer program was written that extracts other zinc binding motifs (non C2H2 'fingers'), overlapping with the classical zinc finger pattern, from the found set of yeast C2H2 fingers. The complete and correct detection of all fingers is a prerequisite for the classification of the yeast zinc finger proteins in functional terms. The detected 53 yeast C2H2 zinc finger proteins do not contain finger clusters with 10 or more repeats, as is frequently found in higher eukaryotes. Only three proteins contain four or more fingers in a cluster. Moreover, nearly all 27 yeast proteins with tandem arrays of two or three finger domains can be classified into nine subgroups with high sequence conservation in their finger clusters, in particular of their DNA recognition helices. These results and application of the recently elaborated finger/DNA recognition rules suggest that the yeast proteins belonging to the same subgroup may recognize identical or very similar DNA sites.

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Selected References

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  • Ginsberg AM, King BO, Roeder RG. Xenopus 5S gene transcription factor, TFIIIA: characterization of a cDNA clone and measurement of RNA levels throughout development. Cell. 1984 Dec;39(3 Pt 2):479–489. [PubMed]
  • Miller J, McLachlan AD, Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun;4(6):1609–1614. [PMC free article] [PubMed]
  • Brown RS, Sander C, Argos P. The primary structure of transcription factor TFIIIA has 12 consecutive repeats. FEBS Lett. 1985 Jul 8;186(2):271–274. [PubMed]
  • Klug A, Schwabe JW. Protein motifs 5. Zinc fingers. FASEB J. 1995 May;9(8):597–604. [PubMed]
  • Kim CA, Berg JM. A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA. Nat Struct Biol. 1996 Nov;3(11):940–945. [PubMed]
  • Greisman HA, Pabo CO. A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science. 1997 Jan 31;275(5300):657–661. [PubMed]
  • Choo Y, Klug A. Physical basis of a protein-DNA recognition code. Curr Opin Struct Biol. 1997 Feb;7(1):117–125. [PubMed]
  • Hoovers JM, Mannens M, John R, Bliek J, van Heyningen V, Porteous DJ, Leschot NJ, Westerveld A, Little PF. High-resolution localization of 69 potential human zinc finger protein genes: a number are clustered. Genomics. 1992 Feb;12(2):254–263. [PubMed]
  • Jacobs GH. Determination of the base recognition positions of zinc fingers from sequence analysis. EMBO J. 1992 Dec;11(12):4507–4517. [PMC free article] [PubMed]
  • Bairoch A, Bucher P, Hofmann K. The PROSITE database, its status in 1995. Nucleic Acids Res. 1996 Jan 1;24(1):189–196. [PMC free article] [PubMed]
  • Schwabe JW, Klug A. Zinc mining for protein domains. Nat Struct Biol. 1994 Jun;1(6):345–349. [PubMed]
  • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. [PMC free article] [PubMed]
  • Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4355–4358. [PMC free article] [PubMed]
  • Kuhner MK, Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol. 1994 May;11(3):459–468. [PubMed]
  • Reddy BA, Etkin LD, Freemont PS. A novel zinc finger coiled-coil domain in a family of nuclear proteins. Trends Biochem Sci. 1992 Sep;17(9):344–345. [PubMed]
  • Aasland R, Gibson TJ, Stewart AF. The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci. 1995 Feb;20(2):56–59. [PubMed]
  • Ponting CP, Blake DJ, Davies KE, Kendrick-Jones J, Winder SJ. ZZ and TAZ: new putative zinc fingers in dystrophin and other proteins. Trends Biochem Sci. 1996 Jan;21(1):11–13. [PubMed]
  • Borden KL, Freemont PS. The RING finger domain: a recent example of a sequence-structure family. Curr Opin Struct Biol. 1996 Jun;6(3):395–401. [PubMed]
  • Werner M, Hermann-Le Denmat S, Treich I, Sentenac A, Thuriaux P. Effect of mutations in a zinc-binding domain of yeast RNA polymerase C (III) on enzyme function and subunit association. Mol Cell Biol. 1992 Mar;12(3):1087–1095. [PMC free article] [PubMed]
  • Humbert S, van Vuuren H, Lutz Y, Hoeijmakers JH, Egly JM, Moncollin V. p44 and p34 subunits of the BTF2/TFIIH transcription factor have homologies with SSL1, a yeast protein involved in DNA repair. EMBO J. 1994 May 15;13(10):2393–2398. [PMC free article] [PubMed]
  • Stahl B, Chou JH, Li C, Südhof TC, Jahn R. Rab3 reversibly recruits rabphilin to synaptic vesicles by a mechanism analogous to raf recruitment by ras. EMBO J. 1996 Apr 15;15(8):1799–1809. [PMC free article] [PubMed]
  • Stenmark H, Aasland R, Toh BH, D'Arrigo A. Endosomal localization of the autoantigen EEA1 is mediated by a zinc-binding FYVE finger. J Biol Chem. 1996 Sep 27;271(39):24048–24054. [PubMed]
  • McIntosh EM, Haynes RH. Sequence and expression of the dCMP deaminase gene (DCD1) of Saccharomyces cerevisiae. Mol Cell Biol. 1986 May;6(5):1711–1721. [PMC free article] [PubMed]
  • Krisak L, Strich R, Winters RS, Hall JP, Mallory MJ, Kreitzer D, Tuan RS, Winter E. SMK1, a developmentally regulated MAP kinase, is required for spore wall assembly in Saccharomyces cerevisiae. Genes Dev. 1994 Sep 15;8(18):2151–2161. [PubMed]
  • Bartel B, Wünning I, Varshavsky A. The recognition component of the N-end rule pathway. EMBO J. 1990 Oct;9(10):3179–3189. [PMC free article] [PubMed]
  • Dohrmann PR, Voth WP, Stillman DJ. Role of negative regulation in promoter specificity of the homologous transcriptional activators Ace2p and Swi5p. Mol Cell Biol. 1996 Apr;16(4):1746–1758. [PMC free article] [PubMed]
  • Martínez-Pastor MT, Marchler G, Schüller C, Marchler-Bauer A, Ruis H, Estruch F. The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J. 1996 May 1;15(9):2227–2235. [PMC free article] [PubMed]
  • Lutfiyya LL, Johnston M. Two zinc-finger-containing repressors are responsible for glucose repression of SUC2 expression. Mol Cell Biol. 1996 Sep;16(9):4790–4797. [PMC free article] [PubMed]

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