Zinc fingers

The term zinc finger was first used to describe a 30‐residue, repeated sequence motif found in an unusually abundant Xenopus transcription factor. It was proposed that each motif is folded around a central zinc ion to form an independent minidomain and that adjacent zinc fingers are combined as modules to make up a DNA‐binding domain with the modules “gripping” the DNA (hence the term finger). We now know that these proposals were correct and that these DNA‐binding motifs are found in many eukaryotic DNA‐binding proteins. More recently, crystal structures of three different complexes between zinc finger domains and their target DNA binding sites have revealed a remarkably simple mode of interaction with DNA. The simplicity of the zinc finger structure, and of its interaction with DNA, is a very striking feature of this protein domain. After the discovery of the zinc finger motif, patterns of potential zinc ligands have been found in several other proteins, some of which also bind to DNA. Structural studies of these domains have revealed how zinc can stabilize quite diverse protein architectures. In total, 10 such small zinc‐binding domains have been studied structurally. These form a diverse collection, but each in turn has been termed a zinc finger motif—although clearly what they have in common is only their zinc‐binding property, which stabilizes an apparently autonomously folded unit.—Klug, A., Schwabe, J. W. R. Zinc fingers. FASEB J. 9, 597‐604 (1995)

[1]  Mark S. Boguski,et al.  Structure and evolution of a human erythroid transcription factor , 1990, Nature.

[2]  A. Klug,et al.  EXAFS study of the zinc-binding sites in the protein transcription factor IIIA , 1986, Nature.

[3]  A M Gronenborn,et al.  NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. , 1993, Science.

[4]  D. Rhodes,et al.  A new approach to the analysis of DNase I footprinting data and its application to the TFIIIA/5S DNA complex. , 1992, Nucleic acids research.

[5]  P E Wright,et al.  Three-dimensional solution structure of a single zinc finger DNA-binding domain. , 1989, Science.

[6]  Michael Carey,et al.  DNA recognition by GAL4: structure of a protein-DNA complex , 1992, Nature.

[7]  S H Kim,et al.  In vitro selection of zinc fingers with altered DNA-binding specificity. , 1994, Biochemistry.

[8]  T. Gibson,et al.  Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis. , 1992, Nucleic acids research.

[9]  C. Pabo,et al.  Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. , 1993, Science.

[10]  G. Jacobs,et al.  Determination of the base recognition positions of zinc fingers from sequence analysis. , 1992, The EMBO journal.

[11]  K. Yamamoto,et al.  Solution structure of the glucocorticoid receptor DNA-binding domain. , 1990, Science.

[12]  R. Evans,et al.  Primary structure and expression of a functional human glucocorticoid receptor cDNA , 1985, Nature.

[13]  A Klug,et al.  Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[14]  A Klug,et al.  Repetitive zinc‐binding domains in the protein transcription factor IIIA from Xenopus oocytes. , 1985, The EMBO journal.

[15]  J R Desjarlais,et al.  Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J. Schwabe,et al.  Solution structure of the DNA-binding domain of the oestrogen receptor. , 1990, Nature.

[17]  C. Pabo,et al.  Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[18]  S. Harrison,et al.  Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster. , 1994, Genes & development.

[19]  C. Pabo,et al.  Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. , 1994, Science.

[20]  R. Klevit,et al.  Solution structure of a zinc finger domain of yeast ADR1 , 1990, Proteins.

[21]  A Klug,et al.  Adjacent zinc-finger motifs in multiple zinc-finger peptides from SWI5 form structurally independent, flexibly linked domains. , 1992, Journal of molecular biology.

[22]  A. Gronenborn,et al.  High-resolution three-dimensional structure of a single zinc finger from a human enhancer binding protein in solution. , 1992, Biochemistry.

[23]  T. Pieler,et al.  RNA and DNA binding zinc fingers in Xenopus TFIIIA , 1992, Cell.

[24]  H. Pelham,et al.  A specific transcription factor that can bind either the 5S RNA gene or 5S RNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[25]  J. Berg,et al.  Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[26]  D Neuhaus,et al.  DNA recognition by the oestrogen receptor: from solution to the crystal. , 1993, Structure.

[27]  John W. R. Schwabe,et al.  The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition , 1993, Nature.

[28]  John W. R. Schwabe,et al.  The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: How receptors discriminate between their response elements , 1993, Cell.

[29]  Zinc‐ and sequence‐dependent binding to nucleic acids by the N‐terminal zinc finger of the HIV‐1 nucleocapsid protein: NMR structure of the complex with the Psi‐site analog, dACGCC , 1993, Protein science : a publication of the Protein Society.

[30]  M. Johnston A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cerevisiae. , 1987, Microbiological reviews.

[31]  T. Rabbitts,et al.  The LIM domain: a new structural motif found in zinc-finger-like proteins. , 1994, Trends in genetics : TIG.

[32]  S. Goff,et al.  Characterization of Moloney murine leukemia virus mutants with single-amino-acid substitutions in the Cys-His box of the nucleocapsid protein , 1989, Journal of virology.

[33]  B. Luisi,et al.  Structure of the C3HC4 domain by 1H-nuclear magnetic resonance spectroscopy. A new structural class of zinc-finger. , 1994, Journal of molecular biology.

[34]  P F Little,et al.  High-resolution localization of 69 potential human zinc finger protein genes: a number are clustered. , 1992, Genomics.

[35]  N. Pavletich,et al.  Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A , 1991, Science.

[36]  A. Klug,et al.  Zinc mining for protein domains , 1994, Nature Structural Biology.

[37]  S. Kliewer,et al.  Structure of the retinoid X receptor alpha DNA binding domain: a helix required for homodimeric DNA binding. , 1993, Science.

[38]  D. Fourmy,et al.  Methionyl-tRNA synthetase zinc binding domain. Three-dimensional structure and homology with rubredoxin and gag retroviral proteins. , 1993, Journal of molecular biology.

[39]  A Klug,et al.  Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[40]  P. Chambon,et al.  Functional domains of the human estrogen receptor , 1987, Cell.

[41]  S. Gozani,et al.  Novel zinc finger motif in the basal transcriptional machinery: three-dimensional NMR studies of the nucleic acid binding domain of transcriptional elongation factor TFIIS. , 1993, Biochemistry.

[42]  K. Umesono,et al.  Determinants of target gene specificity for steroid/thyroid hormone receptors , 1989, Cell.