Roles of active-site residues in catalysis, substrate binding, cooperativity, and the reaction mechanism of the quinoprotein glycine oxidase

J Biol Chem. 2020 May 8;295(19):6472-6481. doi: 10.1074/jbc.RA120.013198. Epub 2020 Mar 31.

Abstract

The quinoprotein glycine oxidase from the marine bacterium Pseudoalteromonas luteoviolacea (PlGoxA) uses a protein-derived cysteine tryptophylquinone (CTQ) cofactor to catalyze conversion of glycine to glyoxylate and ammonia. This homotetrameric enzyme exhibits strong cooperativity toward glycine binding. It is a good model for studying enzyme kinetics and cooperativity, specifically for being able to separate those aspects of protein function through directed mutagenesis. Variant proteins were generated with mutations in four active-site residues, Phe-316, His-583, Tyr-766, and His-767. Structures for glycine-soaked crystals were obtained for each. Different mutations had differential effects on k cat and K 0.5 for catalysis, K 0.5 for substrate binding, and the Hill coefficients describing the steady-state kinetics or substrate binding. Phe-316 and Tyr-766 variants retained catalytic activity, albeit with altered kinetics and cooperativity. Substitutions of His-583 revealed that it is essential for glycine binding, and the structure of H583C PlGoxA had no active-site glycine present in glycine-soaked crystals. The structure of H767A PlGoxA revealed a previously undetected reaction intermediate, a carbinolamine product-reduced CTQ adduct, and exhibited only negligible activity. The results of these experiments, as well as those with the native enzyme and previous variants, enabled construction of a detailed mechanism for the reductive half-reaction of glycine oxidation. This proposed mechanism includes three discrete reaction intermediates that are covalently bound to CTQ during the reaction, two of which have now been structurally characterized by X-ray crystallography.

Keywords: GoxA; LodA-like protein; acid-base chemistry; cooperativity; cysteine tryptophylquinone; enzyme catalysis; enzyme kinetics; enzyme mechanism; oxidase; quinone; site-directed mutagenesis; structure-function.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Oxidoreductases / chemistry*
  • Amino Acid Oxidoreductases / genetics
  • Amino Acid Substitution
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Catalysis
  • Catalytic Domain
  • Crystallography, X-Ray
  • Mutation, Missense
  • Pseudoalteromonas / enzymology*
  • Pseudoalteromonas / genetics
  • Substrate Specificity

Substances

  • Bacterial Proteins
  • Amino Acid Oxidoreductases
  • glycine oxidase

Supplementary concepts

  • Pseudoalteromonas luteoviolacea

Associated data

  • PDB/6EER
  • PDB/6VL7
  • PDB/6VMW
  • PDB/6VMF
  • PDB/6VMV
  • PDB/6BYW