5VN5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1074/jbc.M117.797696
  • Structures With Same Primary Citation

  • 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 ...

    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

    the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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))
Go to UniProtKB:  G2IN02
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
PHENIXrefinement
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 

  • 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