Catalytic mechanism of S-ribosylhomocysteinase (LuxS): stereochemical course and kinetic isotope effect of proton transfer reactions.
S-ribosylhomocysteinase (LuxS) catalyzes the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum sensing molecule. The proposed mechanism involves a series of proton-transfer reactions, which are catalyzed by an Fe2+ ion and two general acids/bases in the LuxS active site, resulting in the migration of the ribose carbonyl group from its C1 to C3 position. Subsequent beta-elimination at C4 and C5 positions completes the catalytic cycle. In this work, the regiochemistry and stereochemical course of the proton transfer reactions were determined by carrying out the reactions using various specifically deuterium-labeled SRH as substrate and analyzing the reaction products by 1H NMR spectroscopy and mass spectrometry. Our data indicate a suprafacial transfer of the ribose C2 proton to its C1 position and the C3 proton to the C2 position during catalysis, whereas the ribose C4 proton is completely washed into solvent. The primary deuterium kinetic isotope effect suggests that the conversion of 2-keto intermediate to 3-keto intermediate is partially rate limiting. However, mutation of Glu-57, the putative second general acid/base in catalysis, to an aspartic acid renders the final beta-elimination step rate limiting.
Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA.
Jinge
J
Zhu
Reena
R
Patel
Dehua
D
Pei
D001412:Bacillus subtilis / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D013437:Carbon-Sulfur Lyases; D002384:Catalysis; D041961:Deuterium Exchange Measurement / Q000379:methods*; D006710:Homocysteine / Q000031:analogs & derivatives / Q000096:biosynthesis; D007700:Kinetics; D009699:N-Glycosyl Hydrolases / Q000737:chemistry* / Q000378:metabolism; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D011487:Protein Conformation; D011522:Protons; D013379:Substrate Specificity; D014733:Vibrio / Q000201:enzymology
D001426:Bacterial Proteins; D011522:Protons; C487472:S-ribosyl-L-homocysteine; D006710:Homocysteine; D009699:N-Glycosyl Hydrolases; D013437:Carbon-Sulfur Lyases; C117753:LuxS protein, Bacteria