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Transcription regulation
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PDB id
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1pyc
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Contents |
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* Residue conservation analysis
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PDB id:
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Transcription regulation
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Title:
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Cyp1 (hap1) DNA-binding domain (residues 60-100), nmr, 15 structures
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Structure:
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Cyp1. Chain: a. Fragment: residues 56 - 126. Synonym: hap1
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Source:
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Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
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NMR struc:
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15 models
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Authors:
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J.Timmerman,A.-L.Vuidepot,F.Bontems,J.-Y.Lallemand, M.Gervais,E.Shechter,B.Guiard
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Key ref:
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J.Timmerman
et al.
(1996).
1H, 15N resonance assignment and three-dimensional structure of CYP1 (HAP1) DNA-binding domain.
J Mol Biol,
259,
792-804.
PubMed id:
DOI:
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Date:
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17-Feb-96
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Release date:
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01-Aug-96
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PROCHECK
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Headers
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References
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P0CS82
(HAP1_YEASX) -
Heme-responsive zinc finger transcription factor HAP1
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Seq:
Struc:
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1483 a.a.
41 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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Gene Ontology (GO) functional annotation
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Cellular component
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nucleus
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1 term
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Biological process
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regulation of transcription, DNA-dependent
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1 term
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Biochemical function
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sequence-specific DNA binding transcription factor activity
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2 terms
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DOI no:
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J Mol Biol
259:792-804
(1996)
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PubMed id:
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1H, 15N resonance assignment and three-dimensional structure of CYP1 (HAP1) DNA-binding domain.
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J.Timmerman,
A.L.Vuidepot,
F.Bontems,
J.Y.Lallemand,
M.Gervais,
E.Shechter,
B.Guiard.
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ABSTRACT
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CYP1(HAP1) is a transcriptional activator involved in the aerobic metabolism of
the yeast Saccharomyces cerevisiae. The amino acid sequence of its DNA-binding
domain suggests that it belongs to the "zinc cluster" class. This
region is indeed characterized by a pattern known to form a bimetal thiolate
cluster where two zinc ions are coordinated by six cysteine residues. Structures
of two such domains, those from GAL4 and PPR1, have been solved as complexes
with DNA. These domains consist of the zinc cluster connected to a dimerization
helix by a linker peptide. They recognize, as a dimer, an inverted repeat of a
CGG motif that is separated by a specific number of bases. Interestingly, the
specificity of that interaction seems not to be due to the interaction between
the cluster region and the DNA but rather to a fine tune between the structure
of the linker peptide and the number of base-pairs separating the two CGGs.
However, the CYP1 target sites fail to display such a consensus sequence. One of
the two CGG sites is poorly conserved and some experiments suggest a direct
rather than an inverted repeat. Using 1H, 15N and 113Cd NMR spectroscopy, we
have undertaken the analysis of the structural properties of the CYP1(56-126)
fragment that consists of the zinc-cluster region, the linker peptide and a part
of the dimerization helix. We have demonstrated that the six cysteine residues
of the peptide chelate two cadmium ions as in GAL4 and PPR1. Fifteen structures
of the zinc-cluster region (residues 60 to 100) were calculated, the linker
peptide and the dimerization helix being unstructured under the conditions of
our study. This region possesses the same overall fold as in GAL4 and PPR1, and
most of the side-chains involved in the interaction with DNA are structurally
conserved. This suggests that the CYP1 zinc-cluster region recognizes a CGG
triplet in the same way as GAL4 and PPR1. In this case, the particular
properties of CYP1 seem to be due to the structure of the linker peptide and/or
of the dimerization helix.
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Selected figure(s)
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Figure 7.
Figure 7. Comparison of the backbone and zinc-cluster geometry of a regular and an alternative structure of CYP1.
(a) CYP1 3: a regular structure; (b) CYP1 15: an alternative structure; (c) superimposition of the two structures.
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Figure 9.
Figure 9. Comparison of the disposition of GAL4, PPR1 and CYP1 side-chains involved in the interaction with the
DNA. Side-chains (yellow sticks) or oxygen backbone atoms (yellow balls) involved in the interaction with the DNA
in (a) GAL4 or (b) PPR1 and (c) corresponding atoms in CYP1.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
259,
792-804)
copyright 1996.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.L.Vuidepot,
F.Bontems,
M.Gervais,
B.Guiard,
E.Shechter,
and
J.Y.Lallemand
(1997).
NMR analysis of CYP1(HAP1) DNA binding domain-CYC1 upstream activation sequence interactions: recognition of a CGG trinucleotide and of an additional thymine 5 bp downstream by the zinc cluster and the N-terminal extremity of the protein.
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Nucleic Acids Res, 25,
3042-3050.
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F.Lenouvel,
I.Nikolaev,
and
B.Felenbok
(1997).
In vitro recognition of specific DNA targets by AlcR, a zinc binuclear cluster activator different from the other proteins of this class.
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J Biol Chem, 272,
15521-15526.
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J.W.Schwabe,
and
D.Rhodes
(1997).
Linkers made to measure.
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Nat Struct Biol, 4,
680-683.
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K.J.Walters,
K.T.Dayie,
R.J.Reece,
M.Ptashne,
and
G.Wagner
(1997).
Structure and mobility of the PUT3 dimer.
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Nat Struct Biol, 4,
744-750.
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PDB code:
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K.Swaminathan,
P.Flynn,
R.J.Reece,
and
R.Marmorstein
(1997).
Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster.
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Nat Struct Biol, 4,
751-759.
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PDB code:
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R.Näit-Kaoudjt,
R.Williams,
B.Guiard,
and
M.Gervais
(1997).
Some DNA targets of the yeast CYP1 transcriptional activator are functionally asymmetric--evidence of two half-sites with different affinities.
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Eur J Biochem, 244,
301-309.
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S.F.Bellon,
K.K.Rodgers,
D.G.Schatz,
J.E.Coleman,
and
T.A.Steitz
(1997).
Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster.
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Nat Struct Biol, 4,
586-591.
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
