5kka - Revision history

OCA at 10:02, 27 September 2023

OCA — Wed, 27 Sep 2023 10:02:24 GMT

←Older revision		Revision as of 10:02, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5kka' size='340' side='right'caption='[[5kka]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5kka' size='340' side='right'caption='[[5kka]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kka]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KKA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kka]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KKA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6V0:[[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+hydrogen+phosphate'>6V0</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]] 1.75Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kkc\|5kkc]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6V0:[[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+hydrogen+phosphate'>6V0</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdh, b3236, JW3205 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5kka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kka OCA], [https://pdbe.org/5kka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kka RCSB], [https://www.ebi.ac.uk/pdbsum/5kka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kka ProSAT]</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=5kka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kka OCA], [~~http~~://pdbe.org/5kka PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kka RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kka PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kka ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MDH_ECOLI MDH_ECOLI]] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_01516]	+	[https://www.uniprot.org/uniprot/MDH_ECOLI MDH_ECOLI] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_01516]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Malate dehydrogenase]]~~	+	[[Category: Lamb AL]]
-	[[Category: Lamb~~, A L~~]]	+	[[Category: Meneely KM]]
-	[[Category: Meneely~~, K M~~]]	+	[[Category: Moran GR]]
-	[[Category: Moran~~, G R]]~~	+
-	~~[[Category: Beta- 6-dihydronicotimide adenine dinucleotide]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Malate]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:44, 27 November 2019

OCA — Wed, 27 Nov 2019 07:44:56 GMT

←Older revision		Revision as of 07:44, 27 November 2019
Line 1:		Line 1:

	==E. coli malate dehydrogenase with the inhibitor 6DHNAD==		==E. coli malate dehydrogenase with the inhibitor 6DHNAD==
-	<StructureSection load='5kka' size='340' side='right' caption='[[5kka]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5kka' size='340' side='right'caption='[[5kka]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kka]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kka]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KKA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6V0:[[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+hydrogen+phosphate'>6V0</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6V0:[[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+hydrogen+phosphate'>6V0</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kkc\|5kkc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kkc\|5kkc]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdh, b3236, JW3205 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5kka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kka OCA], [http://pdbe.org/5kka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kka RCSB], [http://www.ebi.ac.uk/pdbsum/5kka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kka 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=5kka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kka OCA], [http://pdbe.org/5kka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kka RCSB], [http://www.ebi.ac.uk/pdbsum/5kka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kka ProSAT]</span></td></tr>
Line 22:		Line 23:

	==See Also==		==See Also==
-	*[[Malate ~~dehydrogenase~~\|Malate ~~dehydrogenase~~]]	+	*[[Malate Dehydrogenase 3D structures\|Malate Dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Malate dehydrogenase]]		[[Category: Malate dehydrogenase]]
	[[Category: Lamb, A L]]		[[Category: Lamb, A L]]

OCA at 07:32, 6 October 2017

OCA — Fri, 06 Oct 2017 07:32:21 GMT

←Older revision		Revision as of 07:32, 6 October 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5kka" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kka" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Malate dehydrogenase\|Malate dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:17, 2 November 2016

OCA — Wed, 02 Nov 2016 18:17:22 GMT

←Older revision		Revision as of 18:17, 2 November 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kka is ~~ON HOLD until Paper~~ Publication	+	==E. coli malate dehydrogenase with the inhibitor 6DHNAD==
		+	<StructureSection load='5kka' size='340' side='right' caption='[[5kka]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kka]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KKA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6V0:[[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+hydrogen+phosphate'>6V0</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kkc\|5kkc]]</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=5kka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kka OCA], [http://pdbe.org/5kka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kka RCSB], [http://www.ebi.ac.uk/pdbsum/5kka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kka ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MDH_ECOLI MDH_ECOLI]] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_01516]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Renalase catalyzes the oxidation of isomers of beta-NAD(P)H that carry the hydride in the 2 or 6 positions of the nicotinamide base to form beta-NAD(P)+. This activity is thought to alleviate inhibition of multiple beta-NAD(P)-dependent enzymes of primary and secondary metabolism by these isomers. Here we present evidence for a variety of ligand binding phenomena relevant to the function of renalase. We offer evidence of the potential for primary metabolism inhibition with structures of malate dehydrogenase and lactate dehydrogenase bound to the 6-dihydroNAD isomer. The previously observed preference of renalase from Pseudomonas for NAD-derived substrates over those derived from NADP is accounted for by the structure of the enzyme in complex with NADPH. We also show that nicotinamide nucleosides and mononucleotides reduced in the 2- and 6-positions are renalase substrates, but bind weakly. A seven-fold enhancement of acquisition (kred/Kd) for 6-dihydronicotinamide riboside was observed for human renalase in the presence of ADP. However, generally the addition of complement ligands, AMP for mononucleotide or ADP for nucleoside substrates, did not enhance the reductive half-reaction. Non-substrate nicotinamide nucleosides or nucleotides bind weakly suggesting that only beta-NADH and beta-NADPH compete with dinucleotide substrates for access to the active site.

-	~~Authors:~~ Meneely, ~~K.M.~~, Lamb, A.L.~~, Moran, G~~.R.	+	Ligand binding phenomena that pertain to the metabolic function of renalase.,Beaupre BA, Roman JV, Hoag MR, Meneely KM, Silvaggi NR, Lamb AL, Moran GR Arch Biochem Biophys. 2016 Oct 18;612:46-56. doi: 10.1016/j.abb.2016.10.011. PMID:27769837<ref>PMID:27769837</ref>

-	~~Description: E. coli malate dehydrogenase with~~ the ~~inhibitor 6DHNAD~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Lamb, A.L]]	+	<div class="pdbe-citations 5kka" style="background-color:#fffaf0;"></div>
-	[[Category: Meneely, K.M]]	+	== References ==
-	[[Category: Moran, G.R]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Malate dehydrogenase]]
		+	[[Category: Lamb, A L]]
		+	[[Category: Meneely, K M]]
		+	[[Category: Moran, G R]]
		+	[[Category: Beta- 6-dihydronicotimide adenine dinucleotide]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Malate]]
		+	[[Category: Oxidoreductase]]

OCA at 09:22, 14 July 2016

OCA — Thu, 14 Jul 2016 09:22:20 GMT

←Older revision		Revision as of 09:22, 14 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kka is ON HOLD	+	The entry 5kka is ON HOLD until Paper Publication

	Authors: Meneely, K.M., Lamb, A.L., Moran, G.R.		Authors: Meneely, K.M., Lamb, A.L., Moran, G.R.

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

OCA — Wed, 13 Jul 2016 00:28:18 GMT

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

←Older revision

Revision as of 00:28, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kka is ON HOLD Authors: Meneely, K.M., Lamb, A.L., Moran, G.R. Description: E. coli malate dehydrogenase with the inhibitor 6DHNAD [[Category: Unr...

OCA — Wed, 13 Jul 2016 00:28:16 GMT

New page: '''Unreleased structure''' The entry 5kka is ON HOLD Authors: Meneely, K.M., Lamb, A.L., Moran, G.R. Description: E. coli malate dehydrogenase with the inhibitor 6DHNAD [[Category: Unr...

New page

'''Unreleased structure'''

The entry 5kka is ON HOLD

Authors: Meneely, K.M., Lamb, A.L., Moran, G.R.

Description: E. coli malate dehydrogenase with the inhibitor 6DHNAD
[[Category: Unreleased Structures]]
[[Category: Lamb, A.L]]
[[Category: Meneely, K.M]]
[[Category: Moran, G.R]]