5VN5

Crystal structure of LigY from Sphingobium sp. strain SYK-6

Summary for 5VN5

• Entry DOI: 10.2210/pdb5vn5/pdb
• Descriptor: 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase, ZINC ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: amidohydrolase, lignin degradation, meta-cleavage product hydrolase, hydrolase
• Biological source: Sphingobium sp. SYK-6
• Total number of polymer chains: 3
• Total formula weight: 114589.48

Authors

Kuatsjah, E.,Chan, A.C.K.,Kobylarz, M.J.,Murphy, M.E.P.,Eltis, L.D. (deposition date: 2017-04-28, release date: 2017-09-27, Last modification date: 2024-03-13)

Primary citation

Kuatsjah, E.,Chan, A.C.K.,Kobylarz, M.J.,Murphy, M.E.P.,Eltis, L.D.
The bacterialmeta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the alpha / beta-hydrolase superfamily.
J. Biol. Chem., 292:18290-18302, 2017

PubMed Abstract: Strain SYK-6 of the bacterium sp. catabolizes lignin-derived biphenyl via a -cleavage pathway. In this pathway, LigY is proposed to catalyze the hydrolysis of the -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 and / values as 9.3 ± 0.6 s and 2.5 ± 0.2 × 10 m s, respectively. Sequence analyses and a 1.9 Å resolution crystal structure established that LigY belongs to the amidohydrolase superfamily, unlike previously characterized MCP hydrolases, which are serine-dependent enzymes of the α/β-hydrolase superfamily. The active-site architecture of LigY resembled that of α-amino-β-carboxymuconic-ϵ-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 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 -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.

PubMed: 28935670
DOI: 10.1074/jbc.M117.797696

Experimental method

X-RAY DIFFRACTION (1.9 Å)