5fb3 - Revision history

OCA at 09:11, 20 March 2024

2024-03-20T09:11:57Z

←Older revision		Revision as of 09:11, 20 March 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/G1PDH_PYRCJ G1PDH_PYRCJ] Catalyzes the NAD(P)H-dependent reduction of dihydroxyacetonephosphate (DHAP or glycerone phosphate) to glycerol 1-phosphate (G1P). The G1P thus generated is used as the glycerophosphate backbone of phospholipids in the cellular membranes of Archaea.		[https://www.uniprot.org/uniprot/G1PDH_PYRCJ G1PDH_PYRCJ] Catalyzes the NAD(P)H-dependent reduction of dihydroxyacetonephosphate (DHAP or glycerone phosphate) to glycerol 1-phosphate (G1P). The G1P thus generated is used as the glycerophosphate backbone of phospholipids in the cellular membranes of Archaea.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A gene encoding an sn-glycerol-1-phosphate dehydrogenase (G1PDH) was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The gene was overexpressed in Escherichia coli, and its product was purified and characterized. In contrast to conventional G1PDHs, the expressed enzyme showed strong preference for NADH: the reaction rate (Vmax ) with NADPH was only 2.4% of that with NADH. The crystal structure of the enzyme was determined at a resolution of 2.45 A. The asymmetric unit consisted of one homohexamer. Refinement of the structure and HPLC analysis showed the presence of the bound cofactor NADPH in subunits D, E, and F, even though it was not added in the crystallization procedure. The phosphate group at C2' of the adenine ribose of NADPH is tightly held through the five biased hydrogen bonds with Ser40 and Thr42. In comparison with the known G1PDH structure, the NADPH molecule was observed to be pushed away from the normal coenzyme binding site. Interestingly, the S40A/T42A double mutant enzyme acquired much higher reactivity than the wild-type enzyme with NADPH, which suggests that the biased interactions around the C2'-phosphate group make NADPH binding insufficient for catalysis. Our results provide a unique structural basis for coenzyme preference in NAD(P)-dependent dehydrogenases. Proteins 2016. (c) 2016 Wiley Periodicals, Inc.
-
-	Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis.,Hayashi J, Yamamoto K, Yoneda K, Ohshima T, Sakuraba H Proteins. 2016 Sep 12. doi: 10.1002/prot.25161. PMID:27616573<ref>PMID:27616573</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5fb3" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:44, 19 July 2023

2023-07-19T06:44:44Z

←Older revision		Revision as of 06:44, 19 July 2023
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	<StructureSection load='5fb3' size='340' side='right'caption='[[5fb3]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='5fb3' size='340' side='right'caption='[[5fb3]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fb3]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrcj Pyrcj~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FB3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FB3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fb3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_calidifontis_JCM_11548 Pyrobaculum calidifontis JCM 11548]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FB3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.45Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">egsA, Pcal_0566 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=410359 PYRCJ])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/sn-glycerol-1-phosphate_dehydrogenase sn-glycerol-1-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.261 1.1.1.261] </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=5fb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fb3 OCA], [https://pdbe.org/5fb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fb3 RCSB], [https://www.ebi.ac.uk/pdbsum/5fb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fb3 ProSAT]</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=5fb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fb3 OCA], [~~http~~://pdbe.org/5fb3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fb3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fb3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fb3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/G1PDH_PYRCJ G1PDH_PYRCJ]] Catalyzes the NAD(P)H-dependent reduction of dihydroxyacetonephosphate (DHAP or glycerone phosphate) to glycerol 1-phosphate (G1P). The G1P thus generated is used as the glycerophosphate backbone of phospholipids in the cellular membranes of Archaea.	+	[https://www.uniprot.org/uniprot/G1PDH_PYRCJ G1PDH_PYRCJ] Catalyzes the NAD(P)H-dependent reduction of dihydroxyacetonephosphate (DHAP or glycerone phosphate) to glycerol 1-phosphate (G1P). The G1P thus generated is used as the glycerophosphate backbone of phospholipids in the cellular membranes of Archaea.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyrcj]]~~	+	[[Category: Pyrobaculum calidifontis JCM 11548]]
-	~~[[Category: Sn-glycerol-1-phosphate dehydrogenase~~]]	+	[[Category: Hayashi J]]
-	[[Category: Hayashi, J]]	+	[[Category: Ohshima T]]
-	[[Category: Ohshima, T]]	+	[[Category: Sakuraba H]]
-	[[Category: Sakuraba, H]]	+	[[Category: Yamamoto K]]
-	[[Category: Yamamoto, K]]	+	[[Category: Yoneda K]]
-	[[Category: Yoneda, K]]	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 07:14, 19 February 2020

2020-02-19T07:14:54Z

←Older revision		Revision as of 07:14, 19 February 2020
Line 1:		Line 1:

	==Structure of glycerophosphate dehydrogenase in complex with NADPH==		==Structure of glycerophosphate dehydrogenase in complex with NADPH==
-	<StructureSection load='5fb3' size='340' side='right' caption='[[5fb3]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='5fb3' size='340' side='right'caption='[[5fb3]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fb3]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FB3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fb3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrcj Pyrcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FB3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">egsA, Pcal_0566 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=410359 PYRCJ])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/sn-glycerol-1-phosphate_dehydrogenase sn-glycerol-1-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.261 1.1.1.261] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/sn-glycerol-1-phosphate_dehydrogenase sn-glycerol-1-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.261 1.1.1.261] </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=5fb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fb3 OCA], [http://pdbe.org/5fb3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fb3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fb3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fb3 ProSAT]</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=5fb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fb3 OCA], [http://pdbe.org/5fb3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fb3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fb3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fb3 ProSAT]</span></td></tr>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrcj]]
	[[Category: Sn-glycerol-1-phosphate dehydrogenase]]		[[Category: Sn-glycerol-1-phosphate dehydrogenase]]
	[[Category: Hayashi, J]]		[[Category: Hayashi, J]]

OCA at 17:38, 19 October 2016

2016-10-19T17:38:25Z

←Older revision		Revision as of 17:38, 19 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fb3 is ~~ON HOLD until Paper~~ Publication	+	==Structure of glycerophosphate dehydrogenase in complex with NADPH==
		+	<StructureSection load='5fb3' size='340' side='right' caption='[[5fb3]], [[Resolution\|resolution]] 2.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fb3]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FB3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/sn-glycerol-1-phosphate_dehydrogenase sn-glycerol-1-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.261 1.1.1.261] </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=5fb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fb3 OCA], [http://pdbe.org/5fb3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fb3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fb3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fb3 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/G1PDH_PYRCJ G1PDH_PYRCJ]] Catalyzes the NAD(P)H-dependent reduction of dihydroxyacetonephosphate (DHAP or glycerone phosphate) to glycerol 1-phosphate (G1P). The G1P thus generated is used as the glycerophosphate backbone of phospholipids in the cellular membranes of Archaea.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A gene encoding an sn-glycerol-1-phosphate dehydrogenase (G1PDH) was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The gene was overexpressed in Escherichia coli, and its product was purified and characterized. In contrast to conventional G1PDHs, the expressed enzyme showed strong preference for NADH: the reaction rate (Vmax ) with NADPH was only 2.4% of that with NADH. The crystal structure of the enzyme was determined at a resolution of 2.45 A. The asymmetric unit consisted of one homohexamer. Refinement of the structure and HPLC analysis showed the presence of the bound cofactor NADPH in subunits D, E, and F, even though it was not added in the crystallization procedure. The phosphate group at C2' of the adenine ribose of NADPH is tightly held through the five biased hydrogen bonds with Ser40 and Thr42. In comparison with the known G1PDH structure, the NADPH molecule was observed to be pushed away from the normal coenzyme binding site. Interestingly, the S40A/T42A double mutant enzyme acquired much higher reactivity than the wild-type enzyme with NADPH, which suggests that the biased interactions around the C2'-phosphate group make NADPH binding insufficient for catalysis. Our results provide a unique structural basis for coenzyme preference in NAD(P)-dependent dehydrogenases. Proteins 2016. (c) 2016 Wiley Periodicals, Inc.

-	~~Authors: Sakuraba, H~~., Hayashi, J., Yamamoto, K., Yoneda, K., Ohshima, T.	+	Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis.,Hayashi J, Yamamoto K, Yoneda K, Ohshima T, Sakuraba H Proteins. 2016 Sep 12. doi: 10.1002/prot.25161. PMID:27616573<ref>PMID:27616573</ref>

-	~~Description: Structure~~ of ~~glycerophosphate dehydrogenase in complex with NADPH~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Yoneda, K]]~~	+	<div class="pdbe-citations 5fb3" style="background-color:#fffaf0;"></div>
-	~~[[Category: Yamamoto, K]]~~	+	== References ==
-	~~[[Category: Sakuraba, H]]~~	+	<references/>
-	[[Category: ~~Ohshima, T~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Sn-glycerol-1-phosphate dehydrogenase]]
	[[Category: Hayashi, J]]		[[Category: Hayashi, J]]
		+	[[Category: Ohshima, T]]
		+	[[Category: Sakuraba, H]]
		+	[[Category: Yamamoto, K]]
		+	[[Category: Yoneda, K]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

OCA: Protected "5fb3" [edit=sysop:move=sysop]

2015-12-23T11:23:31Z

Protected "5fb3" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:23, 23 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fb3 is ON HOLD until Paper Publication Authors: Sakuraba, H., Hayashi, J., Yamamoto, K., Yoneda, K., Ohshima, T. Description: Structure of glycero...

2015-12-23T11:23:29Z

New page: '''Unreleased structure''' The entry 5fb3 is ON HOLD until Paper Publication Authors: Sakuraba, H., Hayashi, J., Yamamoto, K., Yoneda, K., Ohshima, T. Description: Structure of glycero...

New page

'''Unreleased structure'''

The entry 5fb3 is ON HOLD until Paper Publication

Authors: Sakuraba, H., Hayashi, J., Yamamoto, K., Yoneda, K., Ohshima, T.

Description: Structure of glycerophosphate dehydrogenase in complex with NADPH
[[Category: Unreleased Structures]]
[[Category: Yoneda, K]]
[[Category: Yamamoto, K]]
[[Category: Sakuraba, H]]
[[Category: Ohshima, T]]
[[Category: Hayashi, J]]