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1pyc

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CYP1 (HAP1) DNA-BINDING DOMAIN (RESIDUES 60-100), NMR, 15 STRUCTURES

Structural highlights

1pyc is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gaisne M, Bécam AM, Verdière J, Herbert CJ. A 'natural' mutation in Saccharomyces cerevisiae strains derived from S288c affects the complex regulatory gene HAP1 (CYP1). Curr Genet. 1999 Oct;36(4):195-200. PMID:10541856 doi:10.1007/s002940050490
↑ Hon T, Lee HC, Hach A, Johnson JL, Craig EA, Erdjument-Bromage H, Tempst P, Zhang L. The Hsp70-Ydj1 molecular chaperone represses the activity of the heme activator protein Hap1 in the absence of heme. Mol Cell Biol. 2001 Dec;21(23):7923-32. PMID:11689685 doi:10.1128/MCB.21.23.7923-7932.2001
↑ Creusot F, Verdière J, Gaisne M, Slonimski PP. CYP1 (HAP1) regulator of oxygen-dependent gene expression in yeast. I. Overall organization of the protein sequence displays several novel structural domains. J Mol Biol. 1988 Nov 20;204(2):263-76. PMID:2851658 doi:10.1016/0022-2836(88)90574-8
↑ Zitomer RS, Carrico P, Deckert J. Regulation of hypoxic gene expression in yeast. Kidney Int. 1997 Feb;51(2):507-13. PMID:9027731 doi:10.1038/ki.1997.71
↑ Timmerman J, Vuidepot AL, Bontems F, Lallemand JY, Gervais M, Shechter E, Guiard B. 1H, 15N resonance assignment and three-dimensional structure of CYP1 (HAP1) DNA-binding domain. J Mol Biol. 1996 Jun 21;259(4):792-804. PMID:8683583 doi:10.1006/jmbi.1996.0358

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1pyc"

@@ Line 1: / Line 1: @@
 ==CYP1 (HAP1) DNA-BINDING DOMAIN (RESIDUES 60-100), NMR, 15 STRUCTURES==
-<StructureSection load='1pyc' size='340' side='right'caption='[[1pyc]], [[NMR_Ensembles_of_Models | 15 NMR models]]' scene=''>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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]]
@@ Line 32: / Line 35: @@
 [[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Bontems, F]]
+[[Category: Bontems F]]
-[[Category: Gervais, M]]
+[[Category: Gervais M]]
-[[Category: Guiard, B]]
+[[Category: Guiard B]]
-[[Category: Lallemand, J Y]]
+[[Category: Lallemand J-Y]]
-[[Category: Shechter, E]]
+[[Category: Shechter E]]
-[[Category: Timmerman, J]]
+[[Category: Timmerman J]]
-[[Category: Vuidepot, A L]]
+[[Category: Vuidepot A-L]]
-[[Category: Activator]]
-[[Category: Dna-binding]]
-[[Category: Heme]]
-[[Category: Metal-binding]]
-[[Category: Nuclear protein]]
-[[Category: Transcription regulation]]
-[[Category: Zinc]]

1pyc

From Proteopedia

Current revision

CYP1 (HAP1) DNA-BINDING DOMAIN (RESIDUES 60-100), NMR, 15 STRUCTURES

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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