2d4a - Revision history

OCA at 13:46, 13 March 2024

2024-03-13T13:46:22Z

← Older revision		Revision as of 13:46, 13 March 2024
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	<StructureSection load='2d4a' size='340' side='right'caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='2d4a' size='340' side='right'caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aerpx Aerpx~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4A FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4A FirstGlance]. <br>
	</td></tr><tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>[~~https://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase~~]~~, with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1~~.~~1.37] </span>~~</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]] 2.87Å</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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [https://pdbe.org/2d4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [https://www.ebi.ac.uk/pdbsum/2d4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4a 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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [https://pdbe.org/2d4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [https://www.ebi.ac.uk/pdbsum/2d4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/MDH_AERPE MDH_AERPE]] Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.<ref>PMID:19555779</ref>		[https://www.uniprot.org/uniprot/MDH_AERPE MDH_AERPE] Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.<ref>PMID:19555779</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=2d4a 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=2d4a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Tartrate oxidation activity was found in the crude extract of an aerobic hyperthermophilic archaeon Aeropyrum pernix, and the enzyme was identified as (S)-malate dehydrogenase (MDH), which, when produced in Escherichia coli, was mainly obtained as an inactive inclusion body. The inclusion body was dissolved in 6 M guanidine-HCl and gradually refolded to the active enzyme through dilution of the denaturant. The purified recombinant enzyme consisted of four identical subunits with a molecular mass of about 110 kDa. NADP was preferred as a coenzyme over NAD for (S)-malate oxidation and, unlike MDHs from other sources, this enzyme readily catalyzed the oxidation of (2S,3S)-tartrate and (2S,3R)-tartrate. The tartrate oxidation activity was also observed in MDHs from the hyperthermophilic archaea Methanocaldococcus jannaschii and Archaeoglobus fulgidus, suggesting these hyperthermophilic MDHs loosely bind their substrates. The refolded A. pernix MDH was also crystallized, and the structure was determined at a resolution of 2.9 A. Its overall structure was similar to those of the M. jannaschii, Chloroflexus aurantiacus, Chlorobium vibrioforme and Cryptosporidium parvum [lactate dehydrogenase-like] MDHs with root-mean-square-deviation values between 1.4 and 2.1 A. Consistent with earlier reports, Ala at position 53 was responsible for coenzyme specificity, and the next residue, Arg, was important for NADP binding. Structural comparison revealed that the hyperthermostability of the A. pernix MDH is likely attributable to its smaller cavity volume and larger numbers of ion pairs and ion-pair networks, but the molecular strategy for thermostability may be specific for each enzyme.

	Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.,Kawakami R, Sakuraba H, Goda S, Tsuge H, Ohshima T Biochim Biophys Acta. 2009 Oct;1794(10):1496-504. Epub 2009 Jun 23. PMID:19555779<ref>PMID:19555779</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2d4a" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Aerpx~~]]		[[Category: Aeropyrum pernix]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Malate dehydrogenase]]~~		[[Category: Kawakami R]]
	[[Category: Kawakami, R]]		[[Category: Ohshima T]]
	[[Category: Ohshima, T]]		[[Category: Sakuraba H]]
	[[Category: Sakuraba, H]]		[[Category: Tsuge H]]
	[[Category: Tsuge, H]]
	~~[[Category: Archaea]]~~
	~~[[Category: Hyperthermophile]]~~
	~~[[Category: Oxidoreductase~~]]

OCA at 10:27, 8 December 2021

2021-12-08T10:27:14Z

← Older revision		Revision as of 10:27, 8 December 2021
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	<StructureSection load='2d4a' size='340' side='right'caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='2d4a' size='340' side='right'caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D4A FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4A FirstGlance]. <br>
	</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>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [https://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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [~~http~~://pdbe.org/2d4a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d4a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4a 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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [https://pdbe.org/2d4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [https://www.ebi.ac.uk/pdbsum/2d4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/MDH_AERPE MDH_AERPE]] Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.<ref>PMID:19555779</ref>		[[https://www.uniprot.org/uniprot/MDH_AERPE MDH_AERPE]] Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.<ref>PMID:19555779</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:40, 4 March 2020

2020-03-04T07:40:42Z

← Older revision		Revision as of 07:40, 4 March 2020
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	==Structure of the malate dehydrogenase from Aeropyrum pernix==		==Structure of the malate dehydrogenase from Aeropyrum pernix==
	<StructureSection load='2d4a' size='340' side='right' caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='2d4a' size='340' side='right'caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4A FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4A FirstGlance]. <br>
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	==See Also==		==See Also==
	*[[Malate ~~dehydrogenase~~\|Malate ~~dehydrogenase~~]]		*[[Malate Dehydrogenase 3D structures\|Malate Dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Aerpx]]		[[Category: Aerpx]]
			[[Category: Large Structures]]
	[[Category: Malate dehydrogenase]]		[[Category: Malate dehydrogenase]]
	[[Category: Kawakami, R]]		[[Category: Kawakami, R]]

OCA at 06:22, 30 May 2018

2018-05-30T06:22:56Z

← Older revision		Revision as of 06:22, 30 May 2018
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	==Structure of the malate dehydrogenase from Aeropyrum pernix==		==Structure of the malate dehydrogenase from Aeropyrum pernix==
	<StructureSection load='2d4a' size='340' side='right' caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='2d4a' size='340' side='right' caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4A FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4A FirstGlance]. <br>
	</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>		</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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [http://pdbe.org/2d4a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [http://www.ebi.ac.uk/pdbsum/2d4a 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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [http://pdbe.org/2d4a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [http://www.ebi.ac.uk/pdbsum/2d4a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4a 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/d4/2d4a_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d4/2d4a_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>
	</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=2d4a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:25, 11 September 2015

2015-09-11T08:25:13Z

← Older revision		Revision as of 08:25, 11 September 2015
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	<StructureSection load='2d4a' size='340' side='right' caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='2d4a' size='340' side='right' caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aeropyrum_pernix Aeropyrum pernix~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4A FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4A FirstGlance]. <br>
	</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>		</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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [http://www.ebi.ac.uk/pdbsum/2d4a 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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [http://pdbe.org/2d4a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [http://www.ebi.ac.uk/pdbsum/2d4a PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 2d4a" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Aeropyrum pernix~~]]		[[Category: Aerpx]]
	[[Category: Malate dehydrogenase]]		[[Category: Malate dehydrogenase]]
	[[Category: Kawakami, R]]		[[Category: Kawakami, R]]

OCA at 13:50, 25 December 2014

2014-12-25T13:50:11Z

← Older revision		Revision as of 13:50, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4A FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4A FirstGlance]. <br>
	</td></tr><tr><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>		</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [http://www.ebi.ac.uk/pdbsum/2d4a 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=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [http://www.ebi.ac.uk/pdbsum/2d4a PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/MDH_AERPE MDH_AERPE]] Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.<ref>PMID:19555779</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Malate dehydrogenase]]		[[Category: Malate dehydrogenase]]
	[[Category: Kawakami, R.]]		[[Category: Kawakami, R]]
	[[Category: Ohshima, T.]]		[[Category: Ohshima, T]]
	[[Category: Sakuraba, H.]]		[[Category: Sakuraba, H]]
	[[Category: Tsuge, H.]]		[[Category: Tsuge, H]]
	[[Category: Archaea]]		[[Category: Archaea]]
	[[Category: Hyperthermophile]]		[[Category: Hyperthermophile]]
	~~[[Category: Malate dehydrogenase]]~~
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 05:21, 3 October 2014

2014-10-03T05:21:52Z

← Older revision		Revision as of 05:21, 3 October 2014
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	[[Image:~~2d4a~~.~~png~~\|~~left~~\|~~200px~~]]		==Structure of the malate dehydrogenase from Aeropyrum pernix==
			<StructureSection load='2d4a' size='340' side='right' caption='[[2d4a]], [[Resolution\|resolution]] 2.87Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D4A FirstGlance]. <br>
			</td></tr><tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d4a RCSB], [http://www.ebi.ac.uk/pdbsum/2d4a 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/d4/2d4a_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 ==
			Tartrate oxidation activity was found in the crude extract of an aerobic hyperthermophilic archaeon Aeropyrum pernix, and the enzyme was identified as (S)-malate dehydrogenase (MDH), which, when produced in Escherichia coli, was mainly obtained as an inactive inclusion body. The inclusion body was dissolved in 6 M guanidine-HCl and gradually refolded to the active enzyme through dilution of the denaturant. The purified recombinant enzyme consisted of four identical subunits with a molecular mass of about 110 kDa. NADP was preferred as a coenzyme over NAD for (S)-malate oxidation and, unlike MDHs from other sources, this enzyme readily catalyzed the oxidation of (2S,3S)-tartrate and (2S,3R)-tartrate. The tartrate oxidation activity was also observed in MDHs from the hyperthermophilic archaea Methanocaldococcus jannaschii and Archaeoglobus fulgidus, suggesting these hyperthermophilic MDHs loosely bind their substrates. The refolded A. pernix MDH was also crystallized, and the structure was determined at a resolution of 2.9 A. Its overall structure was similar to those of the M. jannaschii, Chloroflexus aurantiacus, Chlorobium vibrioforme and Cryptosporidium parvum [lactate dehydrogenase-like] MDHs with root-mean-square-deviation values between 1.4 and 2.1 A. Consistent with earlier reports, Ala at position 53 was responsible for coenzyme specificity, and the next residue, Arg, was important for NADP binding. Structural comparison revealed that the hyperthermostability of the A. pernix MDH is likely attributable to its smaller cavity volume and larger numbers of ion pairs and ion-pair networks, but the molecular strategy for thermostability may be specific for each enzyme.

	~~{{STRUCTURE_2d4a\| PDB=2d4a \| SCENE= }}~~		Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.,Kawakami R, Sakuraba H, Goda S, Tsuge H, Ohshima T Biochim Biophys Acta. 2009 Oct;1794(10):1496-504. Epub 2009 Jun 23. PMID:19555779<ref>PMID:19555779</ref>

	~~===Structure~~ of the ~~malate dehydrogenase from Aeropyrum pernix===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_19555779}}~~

	~~==About this Structure==~~
	~~[[2d4a]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aeropyrum_pernix Aeropyrum pernix]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2D4A OCA].~~

	==See Also==		==See Also==
	*[[Johnson sandbox 1\|Johnson sandbox 1]]
	*[[Malate dehydrogenase\|Malate dehydrogenase]]		*[[Malate dehydrogenase\|Malate dehydrogenase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:019555779<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Malate dehydrogenase]]		[[Category: Malate dehydrogenase]]

OCA at 17:27, 20 October 2012

2012-10-20T17:27:21Z

← Older revision		Revision as of 17:27, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[2d4a]] is a 4 chain structure ~~of [[Johnson sandbox 1]] and [[Malate dehydrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA].		[[2d4a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA].

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

OCA at 00:56, 27 July 2012

2012-07-27T00:56:35Z

← Older revision		Revision as of 00:56, 27 July 2012
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	[[Image:2d4a.png\|left\|200px]]		[[Image:2d4a.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2d4a", 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_2d4a\| PDB=2d4a \| SCENE= }}		{{STRUCTURE_2d4a\| PDB=2d4a \| SCENE= }}

	===Structure of the malate dehydrogenase from Aeropyrum pernix===		===Structure of the malate dehydrogenase from Aeropyrum pernix===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_19555779}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 19555779 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_19555779}}		{{ABSTRACT_PUBMED_19555779}}

	==About this Structure==		==About this Structure==
	[[2d4a]] is a 4 chain structure of [[Malate dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA].		[[2d4a]] is a 4 chain structure of [[Johnson sandbox 1]] and [[Malate dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4A OCA].

	==See Also==		==See Also==
	*[[Malate dehydrogenase]]		*[[Johnson sandbox 1\|Johnson sandbox 1]]
			*[[Malate dehydrogenase\|Malate dehydrogenase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~19555779~~</ref><references group="xtra"/>		<ref group="xtra">PMID:019555779</ref><references group="xtra"/>
	[[Category: Aeropyrum pernix]]		[[Category: Aeropyrum pernix]]
	[[Category: Malate dehydrogenase]]		[[Category: Malate dehydrogenase]]

OCA: Protected "2d4a" [edit=sysop:move=sysop]

2010-12-27T01:16:42Z

Protected "2d4a" [edit=sysop:move=sysop]

← Older revision	Revision as of 01:16, 27 December 2010
(No difference)