3rpz - Revision history

OCA at 12:33, 14 March 2024

OCA — Thu, 14 Mar 2024 12:33:12 GMT

←Older revision		Revision as of 12:33, 14 March 2024
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	== Function ==		== Function ==
	[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]		[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]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3rpz" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:46, 17 January 2024

OCA — Wed, 17 Jan 2024 12:46:47 GMT

←Older revision		Revision as of 12:46, 17 January 2024
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	<StructureSection load='3rpz' size='340' side='right'caption='[[3rpz]], [[Resolution\|resolution]] 1.51Å' scene=''>		<StructureSection load='3rpz' size='340' side='right'caption='[[3rpz]], [[Resolution\|resolution]] 1.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rpz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RPZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rpz]] 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=3RPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RPZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NPW:BETA~~-~~6-HYDROXY-1~~,~~4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE+PHOSPHATE'>NPW</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]] 1.51Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1kyh\|1kyh]], [[3rq5\|3rq5]], [[3rq6\|3rq6]], [[3rq8\|3rq8]], [[3rqh\|3rqh]], [[3rqq\|3rqq]], [[3rqx\|3rqx]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NPW:BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE+PHOSPHATE'>NPW</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>BSU38720, yxkO ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1423~~ "~~Vibrio subtilis~~" ~~Ehrenberg 1835])~~<~~/td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/ATP~~-~~dependent_NAD(P)H~~-~~hydrate_dehydratase ATP~~-~~dependent NAD(P)H-hydrate dehydratase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=4.2.1.93 4.2.1.93]~~ </~~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=3rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rpz OCA], [https://pdbe.org/3rpz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rpz RCSB], [https://www.ebi.ac.uk/pdbsum/3rpz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rpz 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=3rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rpz OCA], [https://pdbe.org/3rpz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rpz RCSB], [https://www.ebi.ac.uk/pdbsum/3rpz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rpz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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]	+	[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cymborowski, M]]	+	[[Category: Cymborowski M]]
-	[[Category: Joachimiak, A]]	+	[[Category: Joachimiak A]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Minor W]]
-	[[Category: Minor, W]]	+	[[Category: Shumilin IA]]
-	[[Category: Shumilin~~, I A]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Lyase-lyase substrate complex]]~~	+
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Psi-biology~~]]	+

OCA at 09:58, 13 April 2022

OCA — Wed, 13 Apr 2022 09:58:05 GMT

←Older revision		Revision as of 09:58, 13 April 2022
Line 1:		Line 1:

	==Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH==		==Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH==
-	<StructureSection load='3rpz' size='340' side='right' caption='[[3rpz]], [[Resolution\|resolution]] 1.51Å' scene=''>	+	<StructureSection load='3rpz' size='340' side='right'caption='[[3rpz]], [[Resolution\|resolution]] 1.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rpz]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RPZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RPZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rpz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RPZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NPW:BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE+PHOSPHATE'>NPW</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NPW:BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE+PHOSPHATE'>NPW</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyh\|1kyh]], [[3rq5\|3rq5]], [[3rq6\|3rq6]], [[3rq8\|3rq8]], [[3rqh\|3rqh]], [[3rqq\|3rqq]], [[3rqx\|3rqx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kyh\|1kyh]], [[3rq5\|3rq5]], [[3rq6\|3rq6]], [[3rq8\|3rq8]], [[3rqh\|3rqh]], [[3rqq\|3rqq]], [[3rqx\|3rqx]]</div></td></tr>
-	<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 globigii~~" ~~Migula 1900~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU38720, yxkO ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
-	<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>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/ATP-dependent_NAD(P)H-hydrate_dehydratase ATP-dependent NAD(P)H-hydrate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.93 4.2.1.93] </span></td></tr>
-	<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=3rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rpz OCA], [~~http~~://pdbe.org/3rpz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rpz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rpz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rpz 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=3rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rpz OCA], [https://pdbe.org/3rpz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rpz RCSB], [https://www.ebi.ac.uk/pdbsum/3rpz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rpz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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]	+	[[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Cymborowski, M]]		[[Category: Cymborowski, M]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 13:06, 4 August 2016

OCA — Thu, 04 Aug 2016 13:06:19 GMT

←Older revision		Revision as of 13:06, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH==		==Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH==
	<StructureSection load='3rpz' size='340' side='right' caption='[[3rpz]], [[Resolution\|resolution]] 1.51Å' scene=''>		<StructureSection load='3rpz' size='340' side='right' caption='[[3rpz]], [[Resolution\|resolution]] 1.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rpz]] 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=3RPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RPZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rpz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RPZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NPW:BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE+PHOSPHATE'>NPW</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NPW:BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE+PHOSPHATE'>NPW</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyh\|1kyh]], [[3rq5\|3rq5]], [[3rq6\|3rq6]], [[3rq8\|3rq8]], [[3rqh\|3rqh]], [[3rqq\|3rqq]], [[3rqx\|3rqx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyh\|1kyh]], [[3rq5\|3rq5]], [[3rq6\|3rq6]], [[3rq8\|3rq8]], [[3rqh\|3rqh]], [[3rqq\|3rqq]], [[3rqx\|3rqx]]</td></tr>
-	<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>	+	<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 globigii" Migula 1900])</td></tr>
	<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>		<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>
-	<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=3rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rpz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rpz RCSB], [http://www.ebi.ac.uk/pdbsum/3rpz PDBsum]</span></td></tr>	+	<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=3rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rpz OCA], [http://pdbe.org/3rpz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rpz RCSB], [http://www.ebi.ac.uk/pdbsum/3rpz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rpz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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]	+	[[http://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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3rpz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Cymborowski, M]]		[[Category: Cymborowski, M]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 14:51, 24 December 2014

OCA — Wed, 24 Dec 2014 14:51:16 GMT

←Older revision		Revision as of 14:51, 24 December 2014
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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=3rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rpz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rpz RCSB], [http://www.ebi.ac.uk/pdbsum/3rpz PDBsum]</span></td></tr>		<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=3rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rpz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rpz RCSB], [http://www.ebi.ac.uk/pdbsum/3rpz PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 12:05, 9 December 2014

OCA — Tue, 09 Dec 2014 12:05:46 GMT

←Older revision		Revision as of 12:05, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3rpz.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH==
		+	<StructureSection load='3rpz' size='340' side='right' caption='[[3rpz]], [[Resolution\|resolution]] 1.51Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rpz]] 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=3RPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RPZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NPW:BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE+PHOSPHATE'>NPW</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyh\|1kyh]], [[3rq5\|3rq5]], [[3rq6\|3rq6]], [[3rq8\|3rq8]], [[3rqh\|3rqh]], [[3rqq\|3rqq]], [[3rqx\|3rqx]]</td></tr>
		+	<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>
		+	<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>
		+	<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=3rpz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rpz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rpz RCSB], [http://www.ebi.ac.uk/pdbsum/3rpz PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~{{STRUCTURE_3rpz\| PDB=3rpz \| SCENE= }}~~	+	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>

-	~~===Crystal Structure~~ of ~~ADP~~/~~ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22940582}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[3rpz]] 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=3RPZ OCA].~~	+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: Cymborowski, M.]]	+	[[Category: Cymborowski, M]]
-	[[Category: Joachimiak, A.]]	+	[[Category: Joachimiak, A]]
-	[[Category: ~~MCSG, Midwest Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Minor, W.]]	+	[[Category: Minor, W]]
-	[[Category: Shumilin, I A.]]	+	[[Category: Shumilin, I A]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Lyase-lyase substrate complex]]		[[Category: Lyase-lyase substrate complex]]
	[[Category: Mcsg]]		[[Category: Mcsg]]
-	[[Category: ~~Midwest center for structural genomic]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
	[[Category: Psi-biology]]		[[Category: Psi-biology]]
-	[[Category: Structural genomic]]

OCA at 08:12, 9 January 2013

OCA — Wed, 09 Jan 2013 08:12:14 GMT

←Older revision		Revision as of 08:12, 9 January 2013
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	[[Image:3rpz.png\|left\|200px]]		[[Image:3rpz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3rpz", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3rpz\| PDB=3rpz \| SCENE= }}		{{STRUCTURE_3rpz\| PDB=3rpz \| SCENE= }}

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

		+	{{ABSTRACT_PUBMED_22940582}}

	==About this Structure==		==About this Structure==

OCA at 05:04, 21 September 2011

OCA — Wed, 21 Sep 2011 05:04:30 GMT

←Older revision		Revision as of 05:04, 21 September 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3rpz.png\|left\|200px]]

-	The ~~entry 3rpz~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rpz", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3rpz\| PDB=3rpz \| SCENE= }}

-	~~Authors: Shumilin, I.A., Cymborowski, M., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics~~ (~~MCSG~~)	+	===Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH===

-	~~Description: Crystal~~ Structure ~~of ADP/ATP-dependent NAD(P)H-hydrate dehydratase~~ from Bacillus subtilis co-~~crystallized with ATP~~/~~Mg2+ and soaked with NADPH~~	+
		+	==About this Structure==
		+	[[3rpz]] 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=3RPZ OCA].
		+	[[Category: Bacillus subtilis]]
		+	[[Category: Cymborowski, M.]]
		+	[[Category: Joachimiak, A.]]
		+	[[Category: MCSG, Midwest Center for Structural Genomics.]]
		+	[[Category: Minor, W.]]
		+	[[Category: Shumilin, I A.]]
		+	[[Category: Lyase]]
		+	[[Category: Lyase-lyase substrate complex]]
		+	[[Category: Mcsg]]
		+	[[Category: Midwest center for structural genomic]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi-biology]]
		+	[[Category: Structural genomic]]

OCA at 05:08, 25 May 2011

OCA — Wed, 25 May 2011 05:08:35 GMT

←Older revision		Revision as of 05:08, 25 May 2011
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	The entry 3rpz is ON HOLD		The entry 3rpz is ON HOLD

-	Authors: Shumilin I.A., Cymborowski, M., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)	+	Authors: Shumilin, I.A., Cymborowski, M., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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

OCA: Protected "3rpz" [edit=sysop:move=sysop]

OCA — Wed, 04 May 2011 06:36:04 GMT

Protected "3rpz" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:36, 4 May 2011