1q6q - Revision history

OCA at 06:01, 17 April 2024

OCA — Wed, 17 Apr 2024 06:01:46 GMT

←Older revision		Revision as of 06:01, 17 April 2024
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	<StructureSection load='1q6q' size='340' side='right'caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='1q6q' size='340' side='right'caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=LXP:L~~-~~XYLITOL+5-PHOSPHATE'>LXP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.695Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1q6l\|1q6l]]~~, ~~[[1q6o\|1q6o]], [[1q6r\|1q6r]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [https://pdbe.org/1q6q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [https://www.ebi.ac.uk/pdbsum/1q6q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q6q 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=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [https://pdbe.org/1q6q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [https://www.ebi.ac.uk/pdbsum/1q6q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q6q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ULAD_ECOLI ULAD_ECOLI]] Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.<ref>PMID:11741871</ref>	+	[https://www.uniprot.org/uniprot/ULAD_ECOLI ULAD_ECOLI] Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.<ref>PMID:11741871</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=1q6q 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=1q6q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and orotidine 5'-phosphate decarboxylase (OMPDC) are members of an enzyme suprafamily, the OMPDC suprafamily, because they are homologous enzymes that catalyze mechanistically distinct reactions using different substrates. KGPDC catalyzes the Mg(2+) ion-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to yield L-xylulose 5-phosphate and CO(2); OMPDC catalyzes the metal ion-independent decarboxylation of OMP to UMP and CO(2). Structural studies have shown that KGPDC and OMPDC share several strictly conserved active site residues that are used differently by each enzyme to catalyze their mechanistically distinct reactions. Although the mechanism of the KGPDC-catalyzed reaction has yet to be elucidated, it is thought to proceed via a Mg(2+) ion-stabilized 1,2-enediolate intermediate. Here we report the crystal structures of KGPDC complexed with L-gulonate 6-phosphate, L-threonohydroxamate 4-phosphate, and L-xylitol 5-phosphate, analogues of the substrate, enediolate intermediate, and product, as well as with the product, L-xylulose 5-phosphate, at 1.2, 1.8, 1.7, and 1.8 A resolution, respectively. These structures support a mechanism that involves the formation of a cis-1,2-enediolate intermediate. Contrary to expectations, the geometry of the intermediate does not involve bidentate coordination of both enediolate oxygen atoms to the Mg(2+) ion but rather involves only the coordination of the oxygen on C2 to the Mg(2+) ion. The oxygen atom on C1 instead forms hydrogen bonds to both Lys64 and Asp67, two strictly conserved active site residues. Lys64 also interacts with the oxygen on C2 and may serve to stabilize a cis conformation of the 1,2-enediolate. These structures also implicate His136 to be the general acid that protonates the 1,2-enediolate intermediate. This study further demonstrates that multiple unrelated enzyme functions can evolve from a single active site architecture without regard for substrate binding affinity or mechanism.
-
-	Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.,Wise EL, Yew WS, Gerlt JA, Rayment I Biochemistry. 2003 Oct 28;42(42):12133-42. PMID:14567674<ref>PMID:14567674</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1q6q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Rayment, I]]	+	[[Category: Rayment I]]
-	[[Category: Wise~~, E L~~]]	+	[[Category: Wise EL]]
-	[[Category: Yew~~, W S]]~~	+	[[Category: Yew WS]]
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 06:02, 28 April 2021

OCA — Wed, 28 Apr 2021 06:02:32 GMT

←Older revision		Revision as of 06:02, 28 April 2021
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	<StructureSection load='1q6q' size='340' side='right'caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='1q6q' size='340' side='right'caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6l\|1q6l]], [[1q6o\|1q6o]], [[1q6r\|1q6r]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q6l\|1q6l]], [[1q6o\|1q6o]], [[1q6r\|1q6r]]</div></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=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [~~http~~://pdbe.org/1q6q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1q6q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1q6q 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=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [https://pdbe.org/1q6q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [https://www.ebi.ac.uk/pdbsum/1q6q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q6q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ULAD_ECOLI ULAD_ECOLI]] Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.<ref>PMID:11741871</ref>	+	[[https://www.uniprot.org/uniprot/ULAD_ECOLI ULAD_ECOLI]] Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.<ref>PMID:11741871</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:58, 24 July 2019

OCA — Wed, 24 Jul 2019 06:58:12 GMT

←Older revision		Revision as of 06:58, 24 July 2019
Line 1:		Line 1:

	==Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate==		==Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate==
-	<StructureSection load='1q6q' size='340' side='right' caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>	+	<StructureSection load='1q6q' size='340' side='right'caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]
	[[Category: Rayment, I]]		[[Category: Rayment, I]]

OCA at 08:12, 24 February 2018

OCA — Sat, 24 Feb 2018 08:12:18 GMT

←Older revision		Revision as of 08:12, 24 February 2018
Line 1:		Line 1:
		+
	==Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate==		==Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate==
	<StructureSection load='1q6q' size='340' side='right' caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='1q6q' size='340' side='right' caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6l\|1q6l]], [[1q6o\|1q6o]], [[1q6r\|1q6r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6l\|1q6l]], [[1q6o\|1q6o]], [[1q6r\|1q6r]]</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=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [http://pdbe.org/1q6q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [http://www.ebi.ac.uk/pdbsum/1q6q 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=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [http://pdbe.org/1q6q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [http://www.ebi.ac.uk/pdbsum/1q6q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q6q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q6/1q6q_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q6/1q6q_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 16:52, 8 February 2016

OCA — Mon, 08 Feb 2016 16:52:16 GMT

←Older revision		Revision as of 16:52, 8 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ 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=1q6q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:34, 10 September 2015

OCA — Thu, 10 Sep 2015 13:34:18 GMT

←Older revision		Revision as of 13:34, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1q6q' size='340' side='right' caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='1q6q' size='340' side='right' caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6l\|1q6l]], [[1q6o\|1q6o]], [[1q6r\|1q6r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6l\|1q6l]], [[1q6o\|1q6o]], [[1q6r\|1q6r]]</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=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [http://www.ebi.ac.uk/pdbsum/1q6q 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=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [http://pdbe.org/1q6q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [http://www.ebi.ac.uk/pdbsum/1q6q PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ULAD_ECOLI ULAD_ECOLI]] Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.<ref>PMID:11741871</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	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 1q6q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]
	[[Category: Rayment, I]]		[[Category: Rayment, I]]

OCA at 07:08, 6 January 2015

OCA — Tue, 06 Jan 2015 07:08:50 GMT

←Older revision		Revision as of 07:08, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6l\|1q6l]], [[1q6o\|1q6o]], [[1q6r\|1q6r]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6l\|1q6l]], [[1q6o\|1q6o]], [[1q6r\|1q6r]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [http://www.ebi.ac.uk/pdbsum/1q6q 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=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [http://www.ebi.ac.uk/pdbsum/1q6q PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Rayment, I.]]	+	[[Category: Rayment, I]]
-	[[Category: Wise, E L.]]	+	[[Category: Wise, E L]]
-	[[Category: Yew, W S.]]	+	[[Category: Yew, W S]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 16:03, 29 September 2014

OCA — Mon, 29 Sep 2014 16:03:07 GMT

←Older revision		Revision as of 16:03, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1q6q.~~png~~\|~~left~~\|200px]]	+	==Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate==
		+	<StructureSection load='1q6q' size='340' side='right' caption='[[1q6q]], [[Resolution\|resolution]] 1.69Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1q6q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q6Q FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LXP:L-XYLITOL+5-PHOSPHATE'>LXP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6l\|1q6l]], [[1q6o\|1q6o]], [[1q6r\|1q6r]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q6q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q6q RCSB], [http://www.ebi.ac.uk/pdbsum/1q6q PDBsum]</span></td></tr>
		+	<table>
		+	== 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/q6/1q6q_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and orotidine 5'-phosphate decarboxylase (OMPDC) are members of an enzyme suprafamily, the OMPDC suprafamily, because they are homologous enzymes that catalyze mechanistically distinct reactions using different substrates. KGPDC catalyzes the Mg(2+) ion-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to yield L-xylulose 5-phosphate and CO(2); OMPDC catalyzes the metal ion-independent decarboxylation of OMP to UMP and CO(2). Structural studies have shown that KGPDC and OMPDC share several strictly conserved active site residues that are used differently by each enzyme to catalyze their mechanistically distinct reactions. Although the mechanism of the KGPDC-catalyzed reaction has yet to be elucidated, it is thought to proceed via a Mg(2+) ion-stabilized 1,2-enediolate intermediate. Here we report the crystal structures of KGPDC complexed with L-gulonate 6-phosphate, L-threonohydroxamate 4-phosphate, and L-xylitol 5-phosphate, analogues of the substrate, enediolate intermediate, and product, as well as with the product, L-xylulose 5-phosphate, at 1.2, 1.8, 1.7, and 1.8 A resolution, respectively. These structures support a mechanism that involves the formation of a cis-1,2-enediolate intermediate. Contrary to expectations, the geometry of the intermediate does not involve bidentate coordination of both enediolate oxygen atoms to the Mg(2+) ion but rather involves only the coordination of the oxygen on C2 to the Mg(2+) ion. The oxygen atom on C1 instead forms hydrogen bonds to both Lys64 and Asp67, two strictly conserved active site residues. Lys64 also interacts with the oxygen on C2 and may serve to stabilize a cis conformation of the 1,2-enediolate. These structures also implicate His136 to be the general acid that protonates the 1,2-enediolate intermediate. This study further demonstrates that multiple unrelated enzyme functions can evolve from a single active site architecture without regard for substrate binding affinity or mechanism.

-	~~{{STRUCTURE_1q6q\| PDB=1q6q \| SCENE= }}~~	+	Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.,Wise EL, Yew WS, Gerlt JA, Rayment I Biochemistry. 2003 Oct 28;42(42):12133-42. PMID:14567674<ref>PMID:14567674</ref>

-	~~===Structure~~ of ~~3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14567674}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1q6q]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:014567674<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Gerlt, J A.]]		[[Category: Gerlt, J A.]]

OCA: Protected "1q6q" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2013 09:44:02 GMT

Protected "1q6q" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:44, 2 January 2013

OCA at 09:44, 2 January 2013

OCA — Wed, 02 Jan 2013 09:44:00 GMT

←Older revision		Revision as of 09:44, 2 January 2013
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-	{{Seed}}
	[[Image:1q6q.png\|left\|200px]]		[[Image:1q6q.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1q6q", 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.
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	{{STRUCTURE_1q6q\| PDB=1q6q \| SCENE= }}		{{STRUCTURE_1q6q\| PDB=1q6q \| SCENE= }}

	===Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate===		===Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14567674}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14567674 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_14567674}}		{{ABSTRACT_PUBMED_14567674}}

	==About this Structure==		==About this Structure==
-	~~1Q6Q~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA].	+	[[1q6q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q6Q OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14567674~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014567674</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Gerlt, J A.]]		[[Category: Gerlt, J A.]]
Line 30:		Line 18:
	[[Category: Yew, W S.]]		[[Category: Yew, W S.]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
-		+	[[Category: Lyase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 00:35:26 2009''~~	+