5OMU

Crystal structure of Amycolatopsis cytochrome P450 GcoA in complex with syringol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion.

Mallinson, S.J.B.Machovina, M.M.Silveira, R.L.Garcia-Borras, M.Gallup, N.Johnson, C.W.Allen, M.D.Skaf, M.S.Crowley, M.F.Neidle, E.L.Houk, K.N.Beckham, G.T.DuBois, J.L.McGeehan, J.E.

(2018) Nat Commun 9: 2487-2487

  • DOI: 10.1038/s41467-018-04878-2
  • Primary Citation of Related Structures:  
    5NCB, 5OGX, 5OMR, 5OMS, 5OMU

  • PubMed Abstract: 
  • Microbial aromatic catabolism offers a promising approach to convert lignin, a vast source of renewable carbon, into useful products. Aryl-O-demethylation is an essential biochemical reaction to ultimately catabolize coniferyl and sinapyl lignin-derived aromatic compounds, and is often a key bottleneck for both native and engineered bioconversion pathways ...

    Microbial aromatic catabolism offers a promising approach to convert lignin, a vast source of renewable carbon, into useful products. Aryl-O-demethylation is an essential biochemical reaction to ultimately catabolize coniferyl and sinapyl lignin-derived aromatic compounds, and is often a key bottleneck for both native and engineered bioconversion pathways. Here, we report the comprehensive characterization of a promiscuous P450 aryl-O-demethylase, consisting of a cytochrome P450 protein from the family CYP255A (GcoA) and a three-domain reductase (GcoB) that together represent a new two-component P450 class. Though originally described as converting guaiacol to catechol, we show that this system efficiently demethylates both guaiacol and an unexpectedly wide variety of lignin-relevant monomers. Structural, biochemical, and computational studies of this novel two-component system elucidate the mechanism of its broad substrate specificity, presenting it as a new tool for a critical step in biological lignin conversion.


    Organizational Affiliation

    Molecular Biophysics, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK. john.mcgeehan@port.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450A409Amycolatopsis sp. ATCC 39116Mutation(s): 0 
Gene Names: AMETH_3834
Find proteins for A0A076MY51 (Amycolatopsis methanolica 239)
Explore A0A076MY51 
Go to UniProtKB:  A0A076MY51
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
3DM
Query on 3DM

Download Ideal Coordinates CCD File 
A
2,6-dimethoxyphenol
C8 H10 O3
KLIDCXVFHGNTTM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.36α = 90
b = 105.36β = 90
c = 113.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P0119818/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L001926/1
DOE-BETOUnited StatesDE-AC36-08GO28308

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references