7by9 - Revision history

OCA at 15:40, 29 November 2023

OCA — Wed, 29 Nov 2023 15:40:41 GMT

←Older revision		Revision as of 15:40, 29 November 2023
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	<StructureSection load='7by9' size='340' side='right'caption='[[7by9]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='7by9' size='340' side='right'caption='[[7by9]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7by9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7by9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BY9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</scene>~~, ~~<scene name='pdbligand=OAA:OXALOACETATE+ION'>OAA</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]] 2.2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>mdh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1422 ATCC 12980])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OAA:OXALOACETATE+ION'>OAA</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=7by9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7by9 OCA], [https://pdbe.org/7by9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7by9 RCSB], [https://www.ebi.ac.uk/pdbsum/7by9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7by9 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=7by9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7by9 OCA], [https://pdbe.org/7by9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7by9 RCSB], [https://www.ebi.ac.uk/pdbsum/7by9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7by9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A143T1U9_GEOSE A0A143T1U9_GEOSE]] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]	+	[https://www.uniprot.org/uniprot/A0A143T1U9_GEOSE A0A143T1U9_GEOSE] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980~~]]	+	[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Malate dehydrogenase]]~~	+	[[Category: Himiyama T]]
-	[[Category: Himiyama, T]]	+	[[Category: Nakamura T]]
-	[[Category: Nakamura, T]]	+	[[Category: Nishiya Y]]
-	[[Category: Nishiya, Y]]	+	[[Category: Shimozawa Y]]
-	[[Category: Shimozawa, Y]]	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:47, 16 February 2022

OCA — Wed, 16 Feb 2022 10:47:38 GMT

←Older revision		Revision as of 10:47, 16 February 2022
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	==Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)==		==Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)==
-	<StructureSection load='7by9' size='340' side='right'caption='[[7by9]]' scene=''>	+	<StructureSection load='7by9' size='340' side='right'caption='[[7by9]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7by9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BY9 FirstGlance]. <br>
-	</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=7by9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7by9 OCA], [https://pdbe.org/7by9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7by9 RCSB], [https://www.ebi.ac.uk/pdbsum/7by9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7by9 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OAA:OXALOACETATE+ION'>OAA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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'>[https://proteopedia.org/fgij/fg.htm?mol=7by9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7by9 OCA], [https://pdbe.org/7by9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7by9 RCSB], [https://www.ebi.ac.uk/pdbsum/7by9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7by9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A143T1U9_GEOSE A0A143T1U9_GEOSE]] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Malate dehydrogenase (MDH) catalyzes the reversible reduction of oxaloacetate (OAA) to L-malate using nicotinamide adenine dinucleotide hydrogen (NADH). MDH has two characteristic loops, the mobile loop and the catalytic loop, in the active site. On binding to the substrate, the enzyme undergoes a structural change from the open-form, with an open conformation of the mobile loop, to the closed-form, with the loop in a closed conformation. In this study, three crystals of MDH from a moderate thermophile, Geobacillus stearothermophilus (gs-MDH) were used to determine four different enzyme structures (resolutions, 1.95-2.20 A), each of which was correspondingly assigned to its four catalytic states. Two OAA-unbound structures exhibited the open-form, while the other two OAA-bound structures exhibited both the open- and closed-form. The structural analysis suggested that the binding of OAA to the open-form gs-MDH promotes conformational change in the mobile loop and simultaneously activates the catalytic loop. The mutations on the key amino acid residues involving the proposed catalytic mechanism significantly affected the gs-MDH activity, supporting our hypothesis. These findings contribute to the elucidation of the detailed molecular mechanism underlying the substrate recognition and structural switching during the MDH catalytic cycle.
		+
		+	Structural analysis and reaction mechanism of malate dehydrogenase from Geobacillus stearothermophilus.,Shimozawa Y, Himiyama T, Nakamura T, Nishiya Y J Biochem. 2021 Mar 16. pii: 6173449. doi: 10.1093/jb/mvab027. PMID:33723609<ref>PMID:33723609</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7by9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Malate Dehydrogenase 3D structures\|Malate Dehydrogenase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12980]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Himiyama T]]	+	[[Category: Malate dehydrogenase]]
-	[[Category: Nakamura T]]	+	[[Category: Himiyama, T]]
-	[[Category: Nishiya Y]]	+	[[Category: Nakamura, T]]
-	[[Category: Shimozawa Y]]	+	[[Category: Nishiya, Y]]
		+	[[Category: Shimozawa, Y]]
		+	[[Category: Oxidoreductase]]

OCA at 06:40, 24 March 2021

OCA — Wed, 24 Mar 2021 06:40:13 GMT

←Older revision		Revision as of 06:40, 24 March 2021
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-	'''Unreleased structure'''

-	~~The entry 7by9 is ON HOLD until Paper Publication~~	+	==Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)==
-		+	<StructureSection load='7by9' size='340' side='right'caption='[[7by9]]' scene=''>
-	~~Authors: Shimozawa, Y., Nakamura, T., Himiyama, T., Nishiya, Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BY9 FirstGlance]. <br>
-	~~Description:~~ Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)	+	</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=7by9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7by9 OCA], [https://pdbe.org/7by9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7by9 RCSB], [https://www.ebi.ac.uk/pdbsum/7by9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7by9 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Shimozawa, Y~~]]	+	__TOC__
-	[[Category: ~~Himiyama,~~ T]]	+	</StructureSection>
-	[[Category: Nishiya, Y]]	+	[[Category: Large Structures]]
-	[[Category: ~~Nakamura, T~~]]	+	[[Category: Himiyama T]]
		+	[[Category: Nakamura T]]
		+	[[Category: Nishiya Y]]
		+	[[Category: Shimozawa Y]]

OCA at 04:21, 13 May 2020

OCA — Wed, 13 May 2020 04:21:58 GMT

←Older revision		Revision as of 04:21, 13 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7by9 is ON HOLD	+	The entry 7by9 is ON HOLD until Paper Publication

	Authors: Shimozawa, Y., Nakamura, T., Himiyama, T., Nishiya, Y.		Authors: Shimozawa, Y., Nakamura, T., Himiyama, T., Nishiya, Y.

OCA: Protected "7by9" [edit=sysop:move=sysop]

OCA — Wed, 29 Apr 2020 05:38:00 GMT

Protected "7by9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:38, 29 April 2020

OCA: New page: '''Unreleased structure''' The entry 7by9 is ON HOLD Authors: Shimozawa, Y., Nakamura, T., Himiyama, T., Nishiya, Y. Description: Malate Dehydrogenase from Geobacillus stearothermophil...

OCA — Wed, 29 Apr 2020 05:37:58 GMT

New page: '''Unreleased structure''' The entry 7by9 is ON HOLD Authors: Shimozawa, Y., Nakamura, T., Himiyama, T., Nishiya, Y. Description: Malate Dehydrogenase from Geobacillus stearothermophil...

New page

'''Unreleased structure'''

The entry 7by9 is ON HOLD

Authors: Shimozawa, Y., Nakamura, T., Himiyama, T., Nishiya, Y.

Description: Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)
[[Category: Unreleased Structures]]
[[Category: Shimozawa, Y]]
[[Category: Himiyama, T]]
[[Category: Nishiya, Y]]
[[Category: Nakamura, T]]