5ujk - Revision history

OCA at 13:28, 4 October 2023

2023-10-04T13:28:37Z

←Older revision		Revision as of 13:28, 4 October 2023
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	==Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD==		==Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD==
-	<StructureSection load='5ujk' size='340' side='right' caption='[[5ujk]], [[Resolution\|resolution]] 1.53Å' scene=''>	+	<StructureSection load='5ujk' size='340' side='right'caption='[[5ujk]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ujk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_extorquens"_bassalik_1913 "bacillus~~ extorquens~~" bassalik 1913~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ujk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylorubrum_extorquens Methylorubrum extorquens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UJK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</scene~~>, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.53Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>mdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~408~~ "~~Bacillus extorquens~~" ~~Bassalik 1913])~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37]~~ </~~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=5ujk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujk OCA], [https://pdbe.org/5ujk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ujk RCSB], [https://www.ebi.ac.uk/pdbsum/5ujk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujk 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=5ujk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujk OCA], [~~http~~://pdbe.org/5ujk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ujk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ujk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~MDH_METEP MDH_METEP]~~] Catalyzes the reversible oxidation of malate to oxaloacetate.	+	[https://www.uniprot.org/uniprot/MDH_METEA MDH_METEA] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD(+), and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD(+)-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an alpha-helix to a 310-helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.
		+
		+	Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase.,Gonzalez JM, Marti-Arbona R, Chen JCH, Broom-Peltz B, Unkefer CJ Acta Crystallogr F Struct Biol Commun. 2018 Oct 1;74(Pt 10):610-616. doi:, 10.1107/S2053230X18011809. Epub 2018 Sep 19. PMID:30279311<ref>PMID:30279311</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ujk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Malate ~~dehydrogenase~~\|Malate ~~dehydrogenase~~]]	+	*[[Malate Dehydrogenase 3D structures\|Malate Dehydrogenase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus extorquens bassalik 1913~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Malate dehydrogenase~~]]	+	[[Category: Methylorubrum extorquens]]
-	[[Category: Gonzalez~~, J M]]~~	+	[[Category: Gonzalez JM]]
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Malate]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:52, 14 November 2018

2018-11-14T08:52:30Z

←Older revision		Revision as of 08:52, 14 November 2018
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	<StructureSection load='5ujk' size='340' side='right' caption='[[5ujk]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='5ujk' size='340' side='right' caption='[[5ujk]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ujk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ujk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_extorquens"_bassalik_1913 "bacillus extorquens" bassalik 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UJK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=408 "Bacillus extorquens" Bassalik 1913])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </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=5ujk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujk OCA], [http://pdbe.org/5ujk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ujk RCSB], [http://www.ebi.ac.uk/pdbsum/5ujk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujk 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=5ujk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujk OCA], [http://pdbe.org/5ujk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ujk RCSB], [http://www.ebi.ac.uk/pdbsum/5ujk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujk ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MDH_METEP MDH_METEP]] Catalyzes the reversible oxidation of malate to oxaloacetate.		[[http://www.uniprot.org/uniprot/MDH_METEP MDH_METEP]] Catalyzes the reversible oxidation of malate to oxaloacetate.
		+
		+	==See Also==
		+	*[[Malate dehydrogenase\|Malate dehydrogenase]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus extorquens bassalik 1913]]
	[[Category: Malate dehydrogenase]]		[[Category: Malate dehydrogenase]]
	[[Category: Gonzalez, J M]]		[[Category: Gonzalez, J M]]

OCA at 09:31, 10 March 2017

2017-03-10T09:31:10Z

←Older revision		Revision as of 09:31, 10 March 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5ujk ~~is ON HOLD~~	+	==Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD==
-		+	<StructureSection load='5ujk' size='340' side='right' caption='[[5ujk]], [[Resolution\|resolution]] 1.53Å' scene=''>
-	~~Authors~~: ~~Gonzalez, J~~.M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ujk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UJK FirstGlance]. <br>
-	~~Description~~: Malate dehydrogenase ~~from Methylobacterium extorquens~~, ~~complexed~~ with ~~NAD~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </span></td></tr>
-	[[Category: Gonzalez, J.M]]	+	<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=5ujk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujk OCA], [http://pdbe.org/5ujk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ujk RCSB], [http://www.ebi.ac.uk/pdbsum/5ujk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MDH_METEP MDH_METEP]] Catalyzes the reversible oxidation of malate to oxaloacetate.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Malate dehydrogenase]]
		+	[[Category: Gonzalez, J M]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Malate]]
		+	[[Category: Nad]]
		+	[[Category: Oxidoreductase]]

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

2017-01-25T22:13:43Z

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

←Older revision

Revision as of 22:13, 25 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ujk is ON HOLD Authors: Gonzalez, J.M. Description: Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD [[Category: Unreleas...

2017-01-25T22:13:41Z

New page: '''Unreleased structure''' The entry 5ujk is ON HOLD Authors: Gonzalez, J.M. Description: Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5ujk is ON HOLD

Authors: Gonzalez, J.M.

Description: Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD
[[Category: Unreleased Structures]]
[[Category: Gonzalez, J.M]]