1o8c
From Proteopedia
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| - | [[Image:1o8c.jpg|left|200px]]<br /><applet load="1o8c" size="450" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1o8c, resolution 2.60Å" /> | ||
| - | '''CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH'''<br /> | ||
| - | == | + | ==CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH== |
| - | As part of a structural genomics project on bacterial gene products of | + | <StructureSection load='1o8c' size='340' side='right'caption='[[1o8c]], [[Resolution|resolution]] 2.60Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1o8c]] 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=1O8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O8C FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=1o8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o8c OCA], [https://pdbe.org/1o8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o8c RCSB], [https://www.ebi.ac.uk/pdbsum/1o8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o8c ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/ACUI_ECOLI ACUI_ECOLI] Probably catalyzes the NADPH-dependent reduction of acrylyl-CoA to propanoyl-CoA.<ref>PMID:22563425</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/o8/1o8c_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=1o8c ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | As part of a structural genomics project on bacterial gene products of unknown function, the crystal structures of YhdH, a putative quinone oxidoreductase, and its complex with NADP have been determined at 2.25 and 2.6 A resolution, respectively. The overall fold of YhdH is very similar to that of alcohol dehydrogenases and quinone reductases despite its low sequence identity. The absence of any Zn ion indicates that YdhH is a putative quinone oxidoreductase. YhdH forms a homodimer, with each subunit composed of two domains: a catalytic domain and a coenzyme-binding domain. NADP is bound in a deep cleft formed between the two domains. Large conformational changes occur upon NADP binding, with the two domains closing up to each other and narrowing the NADP-binding cleft. Comparisons of the YdhH active site with those of the quinone oxidoreductases from Escherichia coli and Thermus thermophilus made it possible to identify essential conserved residues as being Asn41, Asp43, Asp64 and Arg318. The active-site size is very narrow and unless an induced fit occurs is accessible only to reagents the size of benzoquinone. | ||
| - | + | Structure of Escherichia coli YhdH, a putative quinone oxidoreductase.,Sulzenbacher G, Roig-Zamboni V, Pagot F, Grisel S, Salomoni A, Valencia C, Campanacci V, Vincentelli R, Tegoni M, Eklund H, Cambillau C Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1855-62. Epub 2004, Sep 23. PMID:15388933<ref>PMID:15388933</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: Escherichia coli]] | + | <div class="pdbe-citations 1o8c" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: Bignon | + | <references/> |
| - | [[Category: Cambillau | + | __TOC__ |
| - | [[Category: Grisel | + | </StructureSection> |
| - | [[Category: Pagot | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Roig-Zamboni | + | [[Category: Large Structures]] |
| - | [[Category: Salamoni | + | [[Category: Bignon C]] |
| - | [[Category: Sulzenbacher | + | [[Category: Cambillau C]] |
| - | [[Category: Tegoni | + | [[Category: Grisel S]] |
| - | [[Category: Valencia | + | [[Category: Pagot F]] |
| - | [[Category: Vincentelli | + | [[Category: Roig-Zamboni V]] |
| - | + | [[Category: Salamoni A]] | |
| - | + | [[Category: Sulzenbacher G]] | |
| - | + | [[Category: Tegoni M]] | |
| - | + | [[Category: Valencia C]] | |
| - | + | [[Category: Vincentelli R]] | |
Current revision
CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH
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