5vn5

Publication Abstract from PubMed

Strain SYK-6 of the bacterium Sphingobium sp. catabolizes lignin-derived biphenyl via a meta-cleavage pathway. In this pathway, LigY is proposed to catalyze the hydrolysis of the meta-cleavage product (MCP) 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoate. Here, we validated this reaction by identifying 5-carboxyvanillate and 4-carboxy-2-hydroxypenta-2,4-dienoate as the products and determined the kcat and kcat/Km values as 9.3 +/- 0.6 s(-1) and 2.5 +/- 0.2 x 10(7) m(-1) s(-1), respectively. Sequence analyses and a 1.9 A resolution crystal structure established that LigY belongs to the amidohydrolase superfamily, unlike previously characterized MCP hydrolases, which are serine-dependent enzymes of the alpha/beta-hydrolase superfamily. The active-site architecture of LigY resembled that of alpha-amino-beta-carboxymuconic--semialdehyde decarboxylase, a class III amidohydrolase, with a single zinc ion coordinated by His-6, His-8, His-179, and Glu-282. Interestingly, we found that LigY lacks the acidic residue proposed to activate water for hydrolysis in other class III amidohydrolases. Moreover, substitution of His-223, a conserved residue proposed to activate water in other amidohydrolases, reduced the kcat to a much lesser extent than what has been reported for other amidohydrolases, suggesting that His-223 has a different role in LigY. Substitution of Arg-72, Tyr-190, Arg-234, or Glu-282 reduced LigY activity over 100-fold. On the basis of these results, we propose a catalytic mechanism involving substrate tautomerization, substrate-assisted activation of water for hydrolysis, and formation of a gem-diol intermediate. This last step diverges from what occurs in serine-dependent MCP hydrolases. This study provides insight into C-C-hydrolyzing enzymes and expands the known range of reactions catalyzed by the amidohydrolase superfamily.

The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the alpha/beta-hydrolase superfamily.,Kuatsjah E, Chan ACK, Kobylarz MJ, Murphy MEP, Eltis LD J Biol Chem. 2017 Nov 3;292(44):18290-18302. doi: 10.1074/jbc.M117.797696. Epub, 2017 Sep 20. PMID:28935670^[1]

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