8EZH

A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase R98A/R100A variant modeled with sulfite-NPN adduct

Summary for 8EZH

• Entry DOI: 10.2210/pdb8ezh/pdb
• Descriptor: Lactate racemase, 1,2-ETHANEDIOL, (4S)-5-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-4-sulfo-1,4-dihydropyridine-3-carbothioic S-acid, ... (8 entities in total)
• Functional Keywords: catalytic activity, isomerase activity, racemase and epimerase activity racemase acting on hydroxy acids and derivatives, isomerase, metal ion binding
• Biological source: Lactiplantibacillus plantarum WCFS1
• Total number of polymer chains: 1
• Total formula weight: 48234.87

Authors

Gatreddi, S.,Hausinger, R.P.,Hu, J. (deposition date: 2022-10-31, release date: 2023-01-25, Last modification date: 2024-11-06)

Primary citation

Gatreddi, S.,Sui, D.,Hausinger, R.P.,Hu, J.
Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor.
Acs Catalysis, 13:1441-1448, 2023

PubMed Abstract: The nickel-pincer nucleotide (NPN) cofactor discovered in lactate racemase from (LarA) is essential for the activities of racemases/epimerases in the highly diverse LarA superfamily. Prior mechanistic studies have established a proton-coupled hydride-transfer mechanism for LarA, but direct evidence showing that hydride attacks the C4 atom in the pyridinium ring of NPN has been lacking. Here, we show that sodium borohydride (NaBH) irreversibly inactivates LarA accompanied by a rapid color change of the enzyme. The altered ultraviolet-visible spectra during NaBH titration supported hydride transfer to C4 of NPN, and the concomitant Ni loss unraveled by mass spectrometry experiments accounted for the irreversible inactivation. High resolution structures of LarA revealed a substantially weakened C-Ni bond in the metastable sulfite-NPN adduct where the NPN cofactor is in the reduced state. These findings allowed us to propose a mechanism of LarA inactivation by NaBH that provides key insights into the enzyme-catalyzed reaction and sheds light on the reactivity of small molecule NPN mimetics.

PubMed: 37886035
DOI: 10.1021/acscatal.2c05461

Experimental method

X-RAY DIFFRACTION (1.99 Å)