6PBP

Pseudopaline Dehydrogenase with (S)-Pseudopaline Soaked 1 hour

Summary for 6PBP

• Entry DOI: 10.2210/pdb6pbp/pdb
• Descriptor: Pseudopaline Dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, N-[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(1H-imidazol-5-yl)ethyl]amino}propyl]-L-glutamic acid, ... (5 entities in total)
• Functional Keywords: opine metallophore dehydrogenase enzyme, biosynthetic protein
• Biological source: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
• Total number of polymer chains: 2
• Total formula weight: 101913.07

Authors

McFarlane, J.S.,Lamb, A.L. (deposition date: 2019-06-14, release date: 2019-10-30, Last modification date: 2023-10-11)

Primary citation

McFarlane, J.S.,Zhang, J.,Wang, S.,Lei, X.,Moran, G.R.,Lamb, A.L.
Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores.
J.Biol.Chem., 294:17988-18001, 2019

PubMed Abstract: Pseudopaline and staphylopine are opine metallophores biosynthesized by and , respectively. The final step in opine metallophore biosynthesis is the condensation of the product of a nicotianamine (NA) synthase reaction ( l-HisNA for pseudopaline and d-HisNA for staphylopine) with an α-keto acid (α-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 ()-stereochemistry at carbon C2 of the α-keto acid (prochiral prior to catalysis). A kinetic analysis using stopped-flow spectrometry with ()- or ()-staphylopine and kinetic and structural analysis with ()- and ()-pseudopaline confirmed catalysis in the reverse direction for only ()-staphylopine and ()-pseudopaline, verifying the stereochemistry of these two opine metallophores. Structural analysis at 1.57-1.85 Å resolution captured the hydrolysis of ()-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.

PubMed: 31615895
DOI: 10.1074/jbc.RA119.011059

Experimental method

X-RAY DIFFRACTION (1.64 Å)