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3rq5

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==Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with CoA==
==Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with CoA==
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<StructureSection load='3rq5' size='340' side='right' caption='[[3rq5]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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<StructureSection load='3rq5' size='340' side='right'caption='[[3rq5]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3rq5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RQ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RQ5 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3rq5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RQ5 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kyh|1kyh]], [[3rpz|3rpz]], [[3rq6|3rq6]], [[3rq8|3rq8]], [[3rqh|3rqh]], [[3rqq|3rqq]], [[3rqx|3rqx]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU38720, yxkO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rq5 OCA], [https://pdbe.org/3rq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rq5 RCSB], [https://www.ebi.ac.uk/pdbsum/3rq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rq5 ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ATP-dependent_NAD(P)H-hydrate_dehydratase ATP-dependent NAD(P)H-hydrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.93 4.2.1.93] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rq5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rq5 RCSB], [http://www.ebi.ac.uk/pdbsum/3rq5 PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/YXKO_BACSU YXKO_BACSU]] Catalyzes the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. Together with NAD(P)HX epimerase, which catalyzes the epimerization of the S- and R-forms, the enzyme allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration (By similarity).[HAMAP-Rule:MF_01965]
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[https://www.uniprot.org/uniprot/NNRD_BACSU NNRD_BACSU] Catalyzes the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. Together with NAD(P)HX epimerase, which catalyzes the epimerization of the S- and R-forms, the enzyme allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration.[HAMAP-Rule:MF_01965]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Proteins of unknown function comprise a significant fraction of sequenced genomes. Defining the roles of these proteins is vital to understanding cellular processes. Here, we describe a method to determine a protein function based on the identification of its natural ligand(s) by the crystallographic screening of the binding of a metabolite library, followed by a focused search in the metabolic space. The method was applied to two protein families with unknown function, PF01256 and YjeF_N. The PF01256 proteins, represented by YxkO from Bacillus subtilis and the C-terminal domain of Tm0922 from Thermotoga maritima, were shown to catalyze ADP/ATP-dependent NAD(P)H-hydrate dehydratation, a previously described orphan activity. The YjeF_N proteins, represented by mouse apolipoprotein A-I binding protein and the N-terminal domain of Tm0922, were found to interact with an adenosine diphosphoribose-related substrate and likely serve as ADP-ribosyltransferases. Crystallographic screening of metabolites serves as an efficient tool in functional analyses of uncharacterized proteins.
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Identification of Unknown Protein Function Using Metabolite Cocktail Screening.,Shumilin IA, Cymborowski M, Chertihin O, Jha KN, Herr JC, Lesley SA, Joachimiak A, Minor W Structure. 2012 Aug 28. PMID:22940582<ref>PMID:22940582</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Cymborowski, M]]
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[[Category: Large Structures]]
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[[Category: Joachimiak, A]]
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[[Category: Cymborowski M]]
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[[Category: Structural genomic]]
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[[Category: Joachimiak A]]
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[[Category: Minor, W]]
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[[Category: Minor W]]
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[[Category: Shumilin, I A]]
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[[Category: Shumilin IA]]
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[[Category: Lyase]]
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[[Category: Lyase-lyase substrate complex]]
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[[Category: Mcsg]]
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[[Category: PSI, Protein structure initiative]]
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[[Category: Psi-biology]]
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Current revision

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with CoA

PDB ID 3rq5

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