ArticleBiochimica et biophysica acta. Proteins and proteomics2026
Ornithine racemase uses a catalytic cysteine.
Article in Biochimica et biophysica acta. Proteins and proteomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Salmonella enterica serover typhimurium expresses an ornithine racemase (OrnR), located in a small operon containing amino acid transporter homologues and D-ornithine/d-lysine decarboxylase. This OrnR is part of a clade that has high identity (>75 %) with other sequences in enterobacteria, but is distant (∼40 % identity) from another clade of OrnR found in anaerobic Firmicutes and actinobacteria. OrnR is a member of the pyridoxal-5'-phosphate (PLP)-dependent alanine racemase (AlaR) superfamily (Fold III), but sequence alignments show that it lacks the catalytic Tyr acid/base of the other racemases. However, the sequences show a conserved cysteine. OrnR shows hyperbolic kinetics in the L → D direction, but exhibits sigmoid kinetics in the D → L direction, with n = 1.8. The structure of OrnR predicted by AlphaFold3 was complexed with PLP-DL-ornithine in silico, minimized, and subjected to molecular dynamics simulation. The resulting structure shows that Cys-164 is in the active site, about 4 Å from the Cα of the external aldimine of L-ornithine, while the NZ of Lys-36 is located about 4 Å below Cα on the D-face. The C164A mutant enzyme has no measurable racemization activity, and does not exchange the α-H of L- or D-ornithine in D
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