6pbn - Revision history

OCA at 07:26, 11 October 2023

OCA — Wed, 11 Oct 2023 07:26:36 GMT

←Older revision		Revision as of 07:26, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6pbn' size='340' side='right'caption='[[6pbn]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='6pbn' size='340' side='right'caption='[[6pbn]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pbn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pbn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PBN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=O77:N-[(3S)-3-amino-3-carboxypropyl]-L-histidine'>O77</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]] 1.65Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA4835 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=O77:N-[(3S)-3-amino-3-carboxypropyl]-L-histidine'>O77</scene></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=6pbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbn OCA], [~~http~~://pdbe.org/6pbn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pbn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pbn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbn 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=6pbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbn OCA], [https://pdbe.org/6pbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pbn RCSB], [https://www.ebi.ac.uk/pdbsum/6pbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ODH_PSEAE ODH_PSEAE] Catalyzes the NAD(P)H-dependent reductive condensation of alpha-ketoglutarate to the intermediate formed by the adjacently encoded enzyme PA4836, namely (2S)-2-amino-4-{[(1S)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino}butanoate, leading to the production of pseudopaline. This is the last step in the biosynthesis of the metallophore pseudopaline, which is involved in the acquisition of nickel and zinc, and thus enables bacterial growth inside the host, where metal access is limited. Therefore, this enzyme probably contributes to Pseudomonas virulence. Can use neither pyruvate nor oxaloacetate in place of alpha-ketoglutarate (PubMed:29091735, PubMed:29618515). Is two-fold more efficient using NADPH than NADH as the electron donor (PubMed:29618515).<ref>PMID:29091735</ref> <ref>PMID:29618515</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Lamb~~, A L~~]]	+	[[Category: Lamb AL]]
-	[[Category: McFarlane~~, J S]]~~	+	[[Category: McFarlane JS]]
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Opine metallophore dehydrogenase enzyme~~]]	+

OCA at 10:45, 4 December 2019

OCA — Wed, 04 Dec 2019 10:45:15 GMT

←Older revision		Revision as of 10:45, 4 December 2019
Line 3:		Line 3:
	<StructureSection load='6pbn' size='340' side='right'caption='[[6pbn]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='6pbn' size='340' side='right'caption='[[6pbn]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pbn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pbn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PBN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=O77:N-[(3S)-3-amino-3-carboxypropyl]-L-histidine'>O77</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=O77:N-[(3S)-3-amino-3-carboxypropyl]-L-histidine'>O77</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA4835 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=6pbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbn OCA], [http://pdbe.org/6pbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pbn RCSB], [http://www.ebi.ac.uk/pdbsum/6pbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbn 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=6pbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbn OCA], [http://pdbe.org/6pbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pbn RCSB], [http://www.ebi.ac.uk/pdbsum/6pbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbn ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pseae]]
	[[Category: Lamb, A L]]		[[Category: Lamb, A L]]
	[[Category: McFarlane, J S]]		[[Category: McFarlane, J S]]
	[[Category: Biosynthetic protein]]		[[Category: Biosynthetic protein]]
	[[Category: Opine metallophore dehydrogenase enzyme]]		[[Category: Opine metallophore dehydrogenase enzyme]]

OCA at 09:07, 30 October 2019

OCA — Wed, 30 Oct 2019 09:07:11 GMT

←Older revision		Revision as of 09:07, 30 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6pbn is ~~ON HOLD until Paper~~ Publication	+	==Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour==
		+	<StructureSection load='6pbn' size='340' side='right'caption='[[6pbn]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6pbn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PBN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=O77:N-[(3S)-3-amino-3-carboxypropyl]-L-histidine'>O77</scene></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=6pbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbn OCA], [http://pdbe.org/6pbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pbn RCSB], [http://www.ebi.ac.uk/pdbsum/6pbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbn ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pseudopaline and staphylopine are opine metallophores biosynthesized by Pseudomonas aeruginosa and Staphylococcus aureus, respectively. The final step in opine metallophore biosynthesis is the condensation of the product of a nicotianamine (NA) synthase reaction (i.e. L-HisNA for pseudopaline and D-HisNA for staphylopine) with an alpha-keto acid (alpha-ketoglutarate for pseudopaline and pyruvate for staphylopine), which is performed by an opine dehydrogenase. We hypothesized that the opine dehydrogenase reaction would be reversible only for the opine metallophore product with (R) stereochemistry at carbon C2 of the alpha-keto acid (prochiral prior to catalysis). A kinetic analysis using stopped-flow spectometetry with (R)- or (S)-staphylopine and kinetic and structural analysis with (R)- and (S)-pseudopaline confirmed catalysis in the reverse direction for only (R)-staphylopine and (R)-pseudopaline, verifying the stereochemistry of these two opine metallophores. Structural analysis at 1.65 - 1.85 A resolution captured the hydrolysis of (R)-pseudopaline and allowed identification of a binding pocket for the L-histidine moiety of pseudopaline formed through a repositioning of Phe-340 and Tyr-289 during the catalytic cycle. Transient-state kinetic analysis revealed an ordered release of NADP+ followed by staphylopine, with staphylopine release being the rate-limiting step in catalysis. Knowledge of the stereochemistry for opine metallophores has implications for future studies involving kinetic analysis, as well as opine metallophore transport, metal coordination, and the generation of chiral amines for pharmaceutical development.

-	~~Authors:~~ McFarlane, J.S., ~~Lamb~~, A.L.	+	Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores.,McFarlane JS, Zhang J, Wang S, Lei X, Moran GR, Lamb AL J Biol Chem. 2019 Oct 15. pii: RA119.011059. doi: 10.1074/jbc.RA119.011059. PMID:31615895<ref>PMID:31615895</ref>

-	~~Description: Pseudopaline Dehydrogenase with (R)~~-~~Pseudopaline Soaked 1 hour~~	+	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 6pbn" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Mcfarlane~~, J.S]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lamb, A L]]
		+	[[Category: McFarlane, J S]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Opine metallophore dehydrogenase enzyme]]

OCA at 04:05, 10 July 2019

OCA — Wed, 10 Jul 2019 04:05:59 GMT

←Older revision		Revision as of 04:05, 10 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pbn is ON HOLD	+	The entry 6pbn is ON HOLD until Paper Publication

	Authors: McFarlane, J.S., Lamb, A.L.		Authors: McFarlane, J.S., Lamb, A.L.

OCA: Protected "6pbn" [edit=sysop:move=sysop]

OCA — Wed, 26 Jun 2019 05:14:22 GMT

Protected "6pbn" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:14, 26 June 2019

OCA: New page: '''Unreleased structure''' The entry 6pbn is ON HOLD Authors: McFarlane, J.S., Lamb, A.L. Description: Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour [[Category: Unrele...

OCA — Wed, 26 Jun 2019 05:14:21 GMT

New page: '''Unreleased structure''' The entry 6pbn is ON HOLD Authors: McFarlane, J.S., Lamb, A.L. Description: Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 6pbn is ON HOLD

Authors: McFarlane, J.S., Lamb, A.L.

Description: Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour
[[Category: Unreleased Structures]]
[[Category: Lamb, A.L]]
[[Category: Mcfarlane, J.S]]