1oj7: Difference between revisions

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<StructureSection load='1oj7' size='340' side='right'caption='[[1oj7]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1oj7' size='340' side='right'caption='[[1oj7]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1oj7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OJ7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1oj7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OJ7 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NZQ:5,6-DIHYDROXY-NADP'>NZQ</scene>, <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">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NZQ:5,6-DIHYDROXY-NADP'>NZQ</scene>, <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=1oj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oj7 OCA], [https://pdbe.org/1oj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oj7 RCSB], [https://www.ebi.ac.uk/pdbsum/1oj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oj7 ProSAT]</span></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=1oj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oj7 OCA], [https://pdbe.org/1oj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oj7 RCSB], [https://www.ebi.ac.uk/pdbsum/1oj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oj7 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/YQHD_ECOLI YQHD_ECOLI] NADP-dependent ADH activity.<ref>PMID:15327949</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1oj7 ConSurf].
</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=1oj7 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In the course of a structural genomics program aiming at solving the structures of Escherichia coli open reading frame (ORF) products of unknown function, we have determined the structure of YqhD at 2.0A resolution using the single wavelength anomalous diffraction method at the Pt edge. The crystal structure of YqhD reveals that it is an NADP-dependent dehydrogenase, a result confirmed by activity measurements with several alcohols. The current interpretation of our findings is that YqhD is an alcohol dehydrogenase (ADH) with preference for alcohols longer than C(3). YqhD is a dimer of 2x387 residues, each monomer being composed of two domains, a Rossmann-type fold and an alpha-helical domain. The crystals contain two dimers in the asymmetric unit. While one of the dimers contains a cofactor in both subunits, only one of the subunits in the second dimer contains it, making it possible to compare bound and unbound active sites. The active site contains a Zn atom, as verified by EXAFS on the crystals. The electron density maps of NADP revealed modifications of the nicotinamide ring by oxygen atoms at positions 5 and 6. Further analysis by electrospray mass spectrometry and comparison with the mass spectra of NADP and NADPH revealed the nature of the modification and the incorporation of two hydroxyl moieties at the 5 and 6 position in the nicotinamide ring, yielding NADPH(OH)(2). These modifications might be due to oxygen stress on an enzyme, which would functionally work under anaerobic conditions.
Crystal structure of E.coli alcohol dehydrogenase YqhD: evidence of a covalently modified NADP coenzyme.,Sulzenbacher G, Alvarez K, Van Den Heuvel RH, Versluis C, Spinelli S, Campanacci V, Valencia C, Cambillau C, Eklund H, Tegoni M J Mol Biol. 2004 Sep 10;342(2):489-502. PMID:15327949<ref>PMID:15327949</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1oj7" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ecoli]]
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bignon, C]]
[[Category: Bignon C]]
[[Category: Cambillau, C]]
[[Category: Cambillau C]]
[[Category: Grisel, S]]
[[Category: Grisel S]]
[[Category: Pagot, F]]
[[Category: Pagot F]]
[[Category: Perrier, S]]
[[Category: Perrier S]]
[[Category: Roig-Zamboni, V]]
[[Category: Roig-Zamboni V]]
[[Category: Salamoni, A]]
[[Category: Salamoni A]]
[[Category: Sulzenbacher, G]]
[[Category: Sulzenbacher G]]
[[Category: Tegoni, M]]
[[Category: Tegoni M]]
[[Category: Valencia, C]]
[[Category: Valencia C]]
[[Category: Vincentelli, R]]
[[Category: Vincentelli R]]
[[Category: Hypothetical oxidoreductase]]
[[Category: Oxidoreductase]]
[[Category: Reductase]]
[[Category: Structural genomic]]

Revision as of 05:48, 17 April 2024

STRUCTURAL GENOMICS, UNKNOWN FUNCTION CRYSTAL STRUCTURE OF E. COLI K-12 YQHD

1oj7, resolution 2.00Å

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