6vmf

From Proteopedia

Crystal structure of the Y766F mutant of GoxA soaked with glycine

Structural highlights

6vmf is a 4 chain structure with sequence from Pseudoalteromonas luteoviolacea DSM 6061. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.24Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A161XU12_9GAMM

Publication Abstract from PubMed

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 homotetremeric enzyme exhibits strong cooperativity towards 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 kcat and K0.5 for catalysis, K0.5 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.

Roles of active site residues in catalysis, substrate binding, cooperativity and the reaction mechanism of the quinoprotein glycine oxidase.,Mamounis KJ, Yukl ET, Davidson VL J Biol Chem. 2020 Mar 31. pii: RA120.013198. doi: 10.1074/jbc.RA120.013198. PMID:32234764^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Mamounis KJ, Yukl ET, Davidson VL. Roles of active site residues in catalysis, substrate binding, cooperativity and the reaction mechanism of the quinoprotein glycine oxidase. J Biol Chem. 2020 Mar 31. pii: RA120.013198. doi: 10.1074/jbc.RA120.013198. PMID:32234764 doi:http://dx.doi.org/10.1074/jbc.RA120.013198