DNA recognition by GAL4: structure of a protein-DNA complex

A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 Å resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn2+-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypep-tide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.

[1]  Nic Jones,et al.  Transcriptional regulation by dimerization: Two sides to an incestuous relationship , 1990, Cell.

[2]  M. Brandriss,et al.  Analysis of constitutive and noninducible mutations of the PUT3 transcriptional activator , 1991, Molecular and cellular biology.

[3]  R. C. Dickson,et al.  Cysteine residues in the zinc finger and amino acids adjacent to the finger are necessary for DNA binding by the LAC9 regulatory protein of Kluyveromyces lactis , 1988, Molecular and cellular biology.

[4]  M. Johnston,et al.  Mutational analysis of the GAL4-encoded transcriptional activator protein of Saccharomyces cerevisiae. , 1988, Genetics.

[5]  A. Laughon,et al.  Primary structure of the Saccharomyces cerevisiae GAL4 gene , 1984, Molecular and cellular biology.

[6]  T. Pan,et al.  Sequential assignments of the 1H NMR resonances of Zn(II)2 and 113Cd(II)2 derivatives of the DNA-binding domain of the GAL4 transcription factor reveal a novel structural motif for specific DNA recognition. , 1991, Biochemistry.

[7]  S. Johnston,et al.  Analysis of the Kluyveromyces lactis positive regulatory gene LAC9 reveals functional homology to, but sequence divergence from, the Saccharomyces cerevisiae GAL4 gene. , 1986, Nucleic acids research.

[8]  H. Samuels,et al.  Interactions among a subfamily of nuclear hormone receptors: the regulatory zipper model. , 1990, Molecular endocrinology.

[9]  George M. Church,et al.  A structure-factor least-squares refinement procedure for macromolecular structures using constrained and restrained parameters , 1977 .

[10]  K. Yamamoto,et al.  Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA , 2003, Nature.

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

[12]  M. Ptashne,et al.  Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. , 1986, Science.

[13]  GAL4 transcription factor is not a "zinc finger" but forms a Zn(II)2Cys6 binuclear cluster. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[14]  N. Xuong,et al.  Refined crystal structure of Cd, Zn metallothionein at 2.0Åresolution , 1991 .

[15]  C. Keleher,et al.  The yeast cell-type-specific repressor α2 acts cooperatively with a non-cell-type-specific protein , 1988, Cell.

[16]  P. S. Kim,et al.  X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. , 1991, Science.

[17]  Brian W. Matthews,et al.  An efficient general-purpose least-squares refinement program for macromolecular structures , 1987 .

[18]  Young-Sun Lin,et al.  GAL4 derivatives function alone and synergistically with mammalian activators in vitro , 1988, Cell.

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

[20]  K. Zhou,et al.  Structure of yeast regulatory gene LEU3 and evidence that LEU3 itself is under general amino acid control , 1987, Nucleic Acids Res..

[21]  E. Dubois,et al.  Nucleotide sequence of the ARGRII regulatory gene and amino acid sequence homologies between ARGRII PPRI and GAL4 regulatory proteins. , 1986, European journal of biochemistry.

[22]  J. Leatherwood,et al.  An amino-terminal fragment of GAL4 binds DNA as a dimer. , 1989, Journal of molecular biology.

[23]  M. Ptashne,et al.  The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80 , 1987, Cell.

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

[25]  L. Guarente,et al.  Functional dissection and sequence of yeast HAP1 activator , 1989, Cell.

[26]  P. Kraulis,et al.  Structure of the DNA-binding domain of zinc GAL4 , 1992, Nature.

[27]  Cynthia Wolberger,et al.  Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. , 1991, Cell.

[28]  R. Losson,et al.  cis- and trans-acting regulatory elements of the yeast URA3 promoter , 1990, Molecular and cellular biology.

[29]  A. Andrianopoulos,et al.  Sequence and functional analysis of the positively acting regulatory gene amdR from Aspergillus nidulans , 1990, Molecular and cellular biology.

[30]  R. C. Dickson,et al.  The C6 zinc finger and adjacent amino acids determine DNA-binding specificity and affinity in the yeast activator proteins LAC9 and PPR1 , 1990, Molecular and cellular biology.

[31]  J. Broach,et al.  Regulation of the galactose pathway in Saccharomyces cerevisiae: induction of uridyl transferase mRNA and dependency on GAL4 gene function. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[32]  G. Bricogne,et al.  Methods and programs for direct‐space exploitation of geometric redundancies , 1976 .

[33]  T. A. Jones,et al.  A graphics model building and refinement system for macromolecules , 1978 .

[34]  J. Corton.  Altering DNA-binding specificity of GAL4 requires sequences adjacent to the zinc finger , 1989, Nature.

[35]  M. Ptashne,et al.  GAL11P: A yeast mutation that potentiates the effect of weak GAL4-derived activators , 1990, Cell.

[36]  Jun Ma,et al.  Deletion analysis of GAL4 defines two transcriptional activating segments , 1987, Cell.

[37]  S. Harrison,et al.  Solution structure of the DNA-binding domain of Cd2-GAL4 from S. cerevisiae , 1992, Nature.

[38]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[39]  M. Ptashne,et al.  Specific DNA binding of GAL4, a positive regulatory protein of yeast , 1985, Cell.

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

[41]  D. Parry,et al.  α‐Helical coiled coils and bundles: How to design an α‐helical protein , 1990 .

[42]  K. Yamamoto,et al.  Regulatory crosstalk at composite response elements. , 1991, Trends in biochemical sciences.

[43]  K. Wüthrich,et al.  Metal co-ordination in rat liver metallothionein-2 prepared with or without reconstitution of the metal clusters, and comparison with rabbit liver metallothionein-2. , 1987, Journal of molecular biology.

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

[45]  T. Pan,et al.  The transcription factor LAC9 from Kluyveromyces lactis-like GAL4 from Saccharomyces cerevisiae forms a Zn(II)2Cys6 binuclear cluster. , 1990, The Journal of biological chemistry.

[46]  K. Nandabalan,et al.  Identification of base and backbone contacts used for DNA sequence recognition and high-affinity binding by LAC9, a transcription activator containing a C6 zinc finger , 1991, Molecular and cellular biology.

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

[48]  David Baltimore,et al.  A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins , 1989, Cell.

[49]  R. Kornberg,et al.  Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. , 1988, Journal of molecular biology.

[50]  R. Kornberg,et al.  Specific protein binding to far upstream activating sequences in polymerase II promoters. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[51]  H. Goldberg,et al.  The DNA binding arm of lambda repressor: critical contacts from a flexible region. , 1991, Science.

[52]  S. McKnight,et al.  The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. , 1988, Science.

[53]  M. Johnston.  Genetic evidence that zinc is an essential co-factor in the DNA binding domain of GAL4 protein , 1987, Nature.

[54]  A. Hawkins,et al.  Isolation and characterization of the positively acting regulatory gene QUTA from Aspergillus nidulans. , 1987, Nucleic acids research.

[55]  R. Losson,et al.  Yeast regulatory gene PPR1. I. Nucleotide sequence, restriction map and codon usage. , 1984, Journal of molecular biology.

[56]  Dana L. Smith,et al.  A molecular mechanism for combinatorial control in yeast: MCM1 protein sets the spacing and orientation of the homeodomains of an α2 dimer , 1992, Cell.

[57]  A. Goffeau,et al.  The multidrug resistance gene PDR1 from Saccharomyces cerevisiae. , 1987, The Journal of biological chemistry.

[58]  N. Giles,et al.  Expression of qa-1F activator protein: identification of upstream binding sites in the qa gene cluster and localization of the DNA-binding domain , 1987, Molecular and cellular biology.