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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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This is version 1.2 of the entry. See complete history


The bacterialmeta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the alpha / beta-hydrolase superfamily.

Kuatsjah, E.Chan, A.C.K.Kobylarz, M.J.Murphy, M.E.P.Eltis, L.D.

(2017) J Biol Chem 292: 18290-18302

  • DOI: https://doi.org/10.1074/jbc.M117.797696
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    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 k cat and k cat / K m values as 9.3 ± 0.6 s -1 and 2.5 ± 0.2 × 10 7 m -1 s -1 , 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 k cat 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.

  • Organizational Affiliation

    From the Genome Science and Technology Program and leltis@mail.ubc.ca.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase
A, B, C
338Sphingobium sp. SYK-6Mutation(s): 0 
Gene Names: ligYSLG_07750
Find proteins for G2IN02 (Sphingobium sp. (strain NBRC 103272 / SYK-6))
Explore G2IN02 
Go to UniProtKB:  G2IN02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2IN02
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.02α = 90
b = 195.361β = 90
c = 178.249γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Genome CanadaCanada2108
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada171359

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence