1pgn - Revision history

OCA at 08:07, 14 February 2024

OCA — Wed, 14 Feb 2024 08:07:52 GMT

←Older revision		Revision as of 08:07, 14 February 2024
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	<StructureSection load='1pgn' size='340' side='right'caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1pgn' size='340' side='right'caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ovis_ammon_aries~~ Ovis ~~ammon~~ aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PGN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PGN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NBP:NICOTINAMIDE+8~~-~~BROMO-ADENINE+DINUCLEOTIDE+PHOSPHATE'>NBP</scene>~~, ~~<scene name='pdbligand=POP:PYROPHOSPHATE+~~2~~-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NBP:NICOTINAMIDE+8-BROMO-ADENINE+DINUCLEOTIDE+PHOSPHATE'>NBP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(NADP(+)-dependent,_decarboxylating) Phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </~~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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [https://pdbe.org/1pgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [https://www.ebi.ac.uk/pdbsum/1pgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pgn 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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [https://pdbe.org/1pgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [https://www.ebi.ac.uk/pdbsum/1pgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pgn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/6PGD_SHEEP 6PGD_SHEEP]] Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH.	+	[https://www.uniprot.org/uniprot/6PGD_SHEEP 6PGD_SHEEP] Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH.
	== 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=1pgn 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=1pgn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: The nicotinamide adenine dinucleotide phosphate (NADP)-dependent oxidative decarboxylase, 6-phosphogluconate dehydrogenase, is a major source of reduced coenzyme for synthesis. Enzymes later in the pentose phosphate pathway convert the reaction product, ribulose 5-phosphate, to ribose 5-phosphate. Crystallographic study of complexes with coenzyme and substrate explain the NADP dependence which determines the enzyme's metabolic role and support the proposed general base-general acid mechanism. RESULTS: The refined structures of binary coenzyme/analogue complexes show that Arg33 is ordered by binding the 2'-phosphate, and provides one face of the adenine site. The nicotinamide, while less tightly bound, is more extended when reduced than when oxidized. All substrate binding residues are conserved; the 3-hydroxyl of 6-phosphogluconate is hydrogen bonded to N zeta of Lys183 and the 3-hydrogen points towards the oxidized nicotinamide. The 6-phosphate replaces a tightly bound sulphate in the apo-enzyme. CONCLUSIONS: NADP specificity is achieved primarily by Arg33 which binds the 2'-phosphate but, in its absence, obscures the adenine pocket. The bound oxidized nicotinamide is syn; hydride transfer from bound substrate to the nicotinamide si- face is achieved with a small movement of the nicotinamide nucleotide. Lys183 may act as general base. A water bound to Gly130 in the coenzyme domain is the most likely acid required in decarboxylation. The dihydronicotinamide ring of NADPH competes for ligands with the 1-carboxyl of 6-phosphogluconate.
-
-	Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism.,Adams MJ, Ellis GH, Gover S, Naylor CE, Phillips C Structure. 1994 Jul 15;2(7):651-68. PMID:7922042<ref>PMID:7922042</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1pgn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[6-phosphogluconate dehydrogenase 3D structures\|6-phosphogluconate dehydrogenase 3D structures]]		*[[6-phosphogluconate dehydrogenase 3D structures\|6-phosphogluconate dehydrogenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ovis ~~ammon~~ aries]]	+	[[Category: Ovis aries]]
-	[[Category: Adams~~, M J~~]]	+	[[Category: Adams MJ]]
-	[[Category: Gover, S]]	+	[[Category: Gover S]]
-	[[Category: Phillips, C]]	+	[[Category: Phillips C]]

OCA at 09:29, 8 September 2021

OCA — Wed, 08 Sep 2021 09:29:36 GMT

←Older revision		Revision as of 09:29, 8 September 2021
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	<StructureSection load='1pgn' size='340' side='right'caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1pgn' size='340' side='right'caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ovis_ammon_aries Ovis ammon aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PGN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ovis_ammon_aries Ovis ammon aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PGN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NBP:NICOTINAMIDE+8-BROMO-ADENINE+DINUCLEOTIDE+PHOSPHATE'>NBP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NBP:NICOTINAMIDE+8-BROMO-ADENINE+DINUCLEOTIDE+PHOSPHATE'>NBP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(NADP(+)-dependent,_decarboxylating) Phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(NADP(+)-dependent,_decarboxylating) Phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [~~http~~://pdbe.org/1pgn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pgn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pgn 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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [https://pdbe.org/1pgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [https://www.ebi.ac.uk/pdbsum/1pgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pgn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/6PGD_SHEEP 6PGD_SHEEP]] Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH.	+	[[https://www.uniprot.org/uniprot/6PGD_SHEEP 6PGD_SHEEP]] Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:48, 27 November 2019

OCA — Wed, 27 Nov 2019 09:48:23 GMT

←Older revision		Revision as of 09:48, 27 November 2019
Line 1:		Line 1:

	==CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM==		==CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM==
-	<StructureSection load='1pgn' size='340' side='right' caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1pgn' size='340' side='right'caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_ammon_aries Ovis ammon aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PGN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_ammon_aries Ovis ammon aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PGN FirstGlance]. <br>
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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/pg/1pgn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/1pgn_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>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1pgn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pgn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[6-phosphogluconate dehydrogenase 3D structures\|6-phosphogluconate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ovis ammon aries]]		[[Category: Ovis ammon aries]]
	[[Category: Adams, M J]]		[[Category: Adams, M J]]
	[[Category: Gover, S]]		[[Category: Gover, S]]
	[[Category: Phillips, C]]		[[Category: Phillips, C]]

OCA at 06:51, 29 November 2017

OCA — Wed, 29 Nov 2017 06:51:22 GMT

←Older revision		Revision as of 06:51, 29 November 2017
Line 1:		Line 1:
		+
	==CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM==		==CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM==
	<StructureSection load='1pgn' size='340' side='right' caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1pgn' size='340' side='right' caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(NADP(+)-dependent,_decarboxylating) Phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(NADP(+)-dependent,_decarboxylating) Phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [http://pdbe.org/1pgn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [http://www.ebi.ac.uk/pdbsum/1pgn 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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [http://pdbe.org/1pgn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [http://www.ebi.ac.uk/pdbsum/1pgn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pgn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=1pgn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1pgn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pgn" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[6-phosphogluconate dehydrogenase\|6-phosphogluconate dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:42, 11 September 2015

OCA — Fri, 11 Sep 2015 21:42:55 GMT

←Older revision		Revision as of 21:42, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1pgn' size='340' side='right' caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1pgn' size='340' side='right' caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Ovis_aries~~ Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PGN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_ammon_aries Ovis ammon aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PGN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NBP:NICOTINAMIDE+8-BROMO-ADENINE+DINUCLEOTIDE+PHOSPHATE'>NBP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NBP:NICOTINAMIDE+8-BROMO-ADENINE+DINUCLEOTIDE+PHOSPHATE'>NBP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(~~decarboxylating~~) Phosphogluconate dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(NADP(+)-dependent,_decarboxylating) Phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [http://www.ebi.ac.uk/pdbsum/1pgn 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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [http://pdbe.org/1pgn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [http://www.ebi.ac.uk/pdbsum/1pgn PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1pgn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ovis aries]]	+	[[Category: Ovis ammon aries]]
	[[Category: Adams, M J]]		[[Category: Adams, M J]]
	[[Category: Gover, S]]		[[Category: Gover, S]]
	[[Category: Phillips, C]]		[[Category: Phillips, C]]

OCA at 20:01, 25 December 2014

OCA — Thu, 25 Dec 2014 20:01:34 GMT

←Older revision		Revision as of 20:01, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PGN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PGN FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NBP:NICOTINAMIDE+8-BROMO-ADENINE+DINUCLEOTIDE+PHOSPHATE'>NBP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NBP:NICOTINAMIDE+8-BROMO-ADENINE+DINUCLEOTIDE+PHOSPHATE'>NBP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(decarboxylating) Phosphogluconate dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(decarboxylating) Phosphogluconate dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </span></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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [http://www.ebi.ac.uk/pdbsum/1pgn 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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [http://www.ebi.ac.uk/pdbsum/1pgn PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/6PGD_SHEEP 6PGD_SHEEP]] Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Ovis aries]]		[[Category: Ovis aries]]
-	[[Category: Adams, M J.]]	+	[[Category: Adams, M J]]
-	[[Category: Gover, S.]]	+	[[Category: Gover, S]]
-	[[Category: Phillips, C.]]	+	[[Category: Phillips, C]]

OCA at 20:49, 28 September 2014

OCA — Sun, 28 Sep 2014 20:49:25 GMT

←Older revision		Revision as of 20:49, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1pgn.~~png~~\|~~left~~\|200px]]	+	==CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM==
		+	<StructureSection load='1pgn' size='340' side='right' caption='[[1pgn]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pgn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PGN FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NBP:NICOTINAMIDE+8-BROMO-ADENINE+DINUCLEOTIDE+PHOSPHATE'>NBP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pgd\|2pgd]], [[1pgo\|1pgo]], [[1pgp\|1pgp]], [[1pgq\|1pgq]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(decarboxylating) Phosphogluconate dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </span></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=1pgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pgn RCSB], [http://www.ebi.ac.uk/pdbsum/1pgn 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/pg/1pgn_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 ==
		+	BACKGROUND: The nicotinamide adenine dinucleotide phosphate (NADP)-dependent oxidative decarboxylase, 6-phosphogluconate dehydrogenase, is a major source of reduced coenzyme for synthesis. Enzymes later in the pentose phosphate pathway convert the reaction product, ribulose 5-phosphate, to ribose 5-phosphate. Crystallographic study of complexes with coenzyme and substrate explain the NADP dependence which determines the enzyme's metabolic role and support the proposed general base-general acid mechanism. RESULTS: The refined structures of binary coenzyme/analogue complexes show that Arg33 is ordered by binding the 2'-phosphate, and provides one face of the adenine site. The nicotinamide, while less tightly bound, is more extended when reduced than when oxidized. All substrate binding residues are conserved; the 3-hydroxyl of 6-phosphogluconate is hydrogen bonded to N zeta of Lys183 and the 3-hydrogen points towards the oxidized nicotinamide. The 6-phosphate replaces a tightly bound sulphate in the apo-enzyme. CONCLUSIONS: NADP specificity is achieved primarily by Arg33 which binds the 2'-phosphate but, in its absence, obscures the adenine pocket. The bound oxidized nicotinamide is syn; hydride transfer from bound substrate to the nicotinamide si- face is achieved with a small movement of the nicotinamide nucleotide. Lys183 may act as general base. A water bound to Gly130 in the coenzyme domain is the most likely acid required in decarboxylation. The dihydronicotinamide ring of NADPH competes for ligands with the 1-carboxyl of 6-phosphogluconate.

-	~~{{STRUCTURE_1pgn\| PDB=1pgn \| SCENE= }}~~	+	Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism.,Adams MJ, Ellis GH, Gover S, Naylor CE, Phillips C Structure. 1994 Jul 15;2(7):651-68. PMID:7922042<ref>PMID:7922042</ref>

-	~~===CRYSTALLOGRAPHIC STUDY OF COENZYME~~, ~~COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7922042}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1pgn]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Ovis_aries Ovis aries]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA].~~	+

	==See Also==		==See Also==
	*[[6-phosphogluconate dehydrogenase\|6-phosphogluconate dehydrogenase]]		*[[6-phosphogluconate dehydrogenase\|6-phosphogluconate dehydrogenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:007922042<~~/~~ref~~><~~ref group="xtra">PMID:009665174</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ovis aries]]		[[Category: Ovis aries]]
	[[Category: Adams, M J.]]		[[Category: Adams, M J.]]
	[[Category: Gover, S.]]		[[Category: Gover, S.]]
	[[Category: Phillips, C.]]		[[Category: Phillips, C.]]

OCA at 20:52, 20 October 2012

OCA — Sat, 20 Oct 2012 20:52:34 GMT

←Older revision		Revision as of 20:52, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1pgn]] is a 1 chain structure ~~of [[6-phosphogluconate dehydrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA].	+	[[1pgn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA].

	==See Also==		==See Also==

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

OCA — Fri, 27 Jul 2012 11:54:02 GMT

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

←Older revision

Revision as of 11:54, 27 July 2012

OCA at 11:54, 27 July 2012

OCA — Fri, 27 Jul 2012 11:54:01 GMT

←Older revision		Revision as of 11:54, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1pgn.png\|left\|200px]]		[[Image:1pgn.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pgn", 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_1pgn\| PDB=1pgn \| SCENE= }}		{{STRUCTURE_1pgn\| PDB=1pgn \| SCENE= }}

	===CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM===		===CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_7922042}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 7922042 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_7922042}}		{{ABSTRACT_PUBMED_7922042}}

	==About this Structure==		==About this Structure==
-	~~1PGN~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA].	+	[[1pgn]] is a 1 chain structure of [[6-phosphogluconate dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGN OCA].
		+
		+	==See Also==
		+	*[[6-phosphogluconate dehydrogenase\|6-phosphogluconate dehydrogenase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~7922042~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:007922042</ref><ref group="xtra">PMID:009665174</ref><references group="xtra"/>
	[[Category: Ovis aries]]		[[Category: Ovis aries]]
	[[Category: Adams, M J.]]		[[Category: Adams, M J.]]
	[[Category: Gover, S.]]		[[Category: Gover, S.]]
	[[Category: Phillips, C.]]		[[Category: Phillips, C.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:30:54 2009''