View source for 1pyc


==CYP1 (HAP1) DNA-BINDING DOMAIN (RESIDUES 60-100), NMR, 15 STRUCTURES==
<StructureSection load='1pyc' size='340' side='right'caption='[[1pyc]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1pyc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PYC FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyc OCA], [https://pdbe.org/1pyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pyc RCSB], [https://www.ebi.ac.uk/pdbsum/1pyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyc ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HAP1_YEASX HAP1_YEASX] Regulation of oxygen dependent gene expression. It modulates the expression of Iso-1 (CYP1) and Iso-2 (CYP3) cytochrome c. In response to heme, promotes transcription of genes encoding functions required for respiration, controlling oxidative damage and repression of anaerobic genes. Binds to the sequence 5'-CGGNNNTNNCGG-3'. Is non-functional in terms of iso-1 cytochrome c expression in strain S288c and its derivatives.<ref>PMID:10541856</ref> <ref>PMID:11689685</ref> <ref>PMID:2851658</ref> <ref>PMID:9027731</ref> 
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/1pyc_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pyc ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.

1H, 15N resonance assignment and three-dimensional structure of CYP1 (HAP1) DNA-binding domain.,Timmerman J, Vuidepot AL, Bontems F, Lallemand JY, Gervais M, Shechter E, Guiard B J Mol Biol. 1996 Jun 21;259(4):792-804. PMID:8683583<ref>PMID:8683583</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1pyc" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Bontems F]]
[[Category: Gervais M]]
[[Category: Guiard B]]
[[Category: Lallemand J-Y]]
[[Category: Shechter E]]
[[Category: Timmerman J]]
[[Category: Vuidepot A-L]]