6OJT

Crystal structure of Sphingomonas paucimobilis TMY1009 LsdA phenylazophenol complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1074/jbc.RA119.009428
  • Structures With Same Primary Citation

  • 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 ...

    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

    Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lignostilbene-alpha,beta-dioxygenase isozyme I
A, B
481Sphingomonas paucimobilisMutation(s): 0 
EC: 1.13.11.43
Find proteins for Q53353 (Sphingomonas paucimobilis)
Go to UniProtKB:  Q53353
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NSL
Query on NSL

Download CCD File 
A, B
4-Hydroxyazobenzene
C12 H10 N2 O
BEYOBVMPDRKTNR-BUHFOSPRSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.909α = 90
b = 181.909β = 90
c = 96.431γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



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 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Derived calculations
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence