Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism

Biochemistry. 2018 Jun 12;57(23):3244-3251. doi: 10.1021/acs.biochem.8b00100. Epub 2018 Mar 9.

Abstract

Lactate racemase (LarA) of Lactobacillus plantarum contains a novel organometallic cofactor with nickel coordinated to a covalently tethered pincer ligand, pyridinium-3-thioamide-5-thiocarboxylic acid mononucleotide, but its function in the enzyme mechanism has not been elucidated. This study presents direct evidence that the nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization. No signal was detected by electron paramagnetic resonance spectroscopy for LarA in the absence or presence of substrate, consistent with a +2 metal oxidation state and inconsistent with a previously proposed proton-coupled electron transfer mechanism. Pyruvate, the predicted intermediate for a PCHT mechanism, was observed in quenched solutions of LarA. A normal substrate kinetic isotope effect ( kH/ kD of 3.11 ± 0.17) was established using 2-α-2H-lactate, further supporting a PCHT mechanism. UV-visible spectroscopy revealed a lactate-induced perturbation of the cofactor spectrum, notably increasing the absorbance at 340 nm, and demonstrated an interaction of the cofactor with the inhibitor sulfite. A crystal structure of LarA provided greater resolution (2.4 Å) than previously reported and revealed sulfite binding to the pyridinium C4 atom of the reduced pincer cofactor, mimicking hydride reduction during a PCHT catalytic cycle. Finally, computational modeling supports hydride transfer to the cofactor at the C4 position or to the nickel atom, but with formation of a nickel-hydride species requiring dissociation of the His200 metal ligand. In aggregate, these studies provide compelling evidence that the nickel-pincer cofactor acts by a PCHT mechanism.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Coenzymes / chemistry*
  • Coenzymes / genetics
  • Coenzymes / metabolism
  • Crystallography, X-Ray
  • Electron Spin Resonance Spectroscopy
  • Lactobacillus plantarum / enzymology*
  • Lactobacillus plantarum / genetics
  • Nickel / chemistry*
  • Nickel / metabolism
  • Organometallic Compounds / chemistry*
  • Organometallic Compounds / metabolism
  • Protein Domains
  • Protons*
  • Racemases and Epimerases / chemistry*
  • Racemases and Epimerases / genetics
  • Spectrophotometry, Ultraviolet

Substances

  • Bacterial Proteins
  • Coenzymes
  • Organometallic Compounds
  • Protons
  • Nickel
  • Racemases and Epimerases
  • lactate racemase