Crystal structure of Sphingomonas paucimobilis TMY1009 apo-LsdA

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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This is version 1.3 of the entry. See complete history


Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase.

Kuatsjah, E.Verstraete, M.M.Kobylarz, M.J.Liu, A.K.N.Murphy, M.E.P.Eltis, L.D.

(2019) J Biol Chem 294: 12911-12920

  • DOI: https://doi.org/10.1074/jbc.RA119.009428
  • Primary Citation of Related Structures:  
    6OJR, 6OJT, 6OJW

  • PubMed Abstract: 

    Lignostilbene-α,β-dioxygenase A (LsdA) from the bacterium Sphingomonas paucimobilis TMY1009 is a nonheme iron oxygenase that catalyzes the cleavage of lignostilbene, a compound arising in lignin transformation, to two vanillin molecules. To examine LsdA's substrate specificity, we heterologously produced the dimeric enzyme with the help of chaperones. When tested on several substituted stilbenes, LsdA exhibited the greatest specificity for lignostilbene ( k cat app = 1.00 ± 0.04 × 10 6 m -1 s -1 ). These experiments further indicated that the substrate's 4-hydroxy moiety is required for catalysis and that this moiety cannot be replaced with a methoxy group. Phenylazophenol inhibited the LsdA-catalyzed cleavage of lignostilbene in a reversible, mixed fashion ( K ic = 6 ± 1 μm, K iu = 24 ± 4 μm). An X-ray crystal structure of LsdA at 2.3 Å resolution revealed a seven-bladed β-propeller fold with an iron cofactor coordinated by four histidines, in agreement with previous observations on related carotenoid cleavage oxygenases. We noted that residues at the dimer interface are also present in LsdB, another lignostilbene dioxygenase in S. paucimobilis TMY1009, rationalizing LsdA and LsdB homo- and heterodimerization in vivo A structure of an LsdA·phenylazophenol complex identified Phe 59 , Tyr 101 , and Lys 134 as contacting the 4-hydroxyphenyl moiety of the inhibitor. Phe 59 and Tyr 101 substitutions with His and Phe, respectively, reduced LsdA activity ( k cat app ) ∼15- and 10-fold. The K134M variant did not detectably cleave lignostilbene, indicating that Lys 134 plays a key catalytic role. This study expands our mechanistic understanding of LsdA and related stilbene-cleaving dioxygenases.

  • Organizational Affiliation

    Genome Science and Technology Program, The University of British Columbia, Vancouver V6T 1Z3, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lignostilbene-alpha,beta-dioxygenase isozyme I
A, B
482Sphingomonas paucimobilisMutation(s): 0 
Find proteins for Q53353 (Sphingomonas paucimobilis)
Explore Q53353 
Go to UniProtKB:  Q53353
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53353
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.364α = 90
b = 181.364β = 90
c = 94.983γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada171359
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada04802

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description