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6pbn

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Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour

Structural highlights

6pbn is a 2 chain structure with sequence from Pseudomonas aeruginosa PAO1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.65Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2]

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.

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ McFarlane JS, Lamb AL. Biosynthesis of an Opine Metallophore by Pseudomonas aeruginosa. Biochemistry. 2017 Nov 14;56(45):5967-5971. PMID:29091735 doi:10.1021/acs.biochem.7b00804
↑ McFarlane JS, Davis CL, Lamb AL. Staphylopine, pseudopaline and yersinopine dehydrogenases: a structural and kinetic analysis of a new functional class of opine dehydrogenase. J Biol Chem. 2018 Apr 4. pii: RA118.002007. doi: 10.1074/jbc.RA118.002007. PMID:29618515 doi:http://dx.doi.org/10.1074/jbc.RA118.002007
↑ McFarlane JS, Zhang J, Wang S, Lei X, Moran GR, Lamb AL. Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores. J Biol Chem. 2019 Oct 15. pii: RA119.011059. doi: 10.1074/jbc.RA119.011059. PMID:31615895 doi:http://dx.doi.org/10.1074/jbc.RA119.011059

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6pbn"

Categories: Large Structures | Pseudomonas aeruginosa PAO1 | Lamb AL | McFarlane JS

@@ Line 3: / Line 3: @@
 <StructureSection load='6pbn' size='340' side='right'caption='[[6pbn]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == 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]] 1.65&#8491;</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>
+== 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;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[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]]

6pbn

From Proteopedia

Current revision

Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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