Crystal structure of Amycolatopsis cytochrome P450 GcoA in complex with vanillin.

Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

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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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GcoA409Amycolatopsis sp. ATCC 39116Mutation(s): 0 
Find proteins for A0A3B6UEE9 (Amycolatopsis sp. (strain ATCC 39116 / 75iv2))
Explore A0A3B6UEE9 
Go to UniProtKB:  A0A3B6UEE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3B6UEE9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C34 H32 Fe N4 O4
Query on V55

Download Ideal Coordinates CCD File 
C [auth A]4-hydroxy-3-methoxybenzaldehyde
C8 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.11α = 90
b = 104.11β = 90
c = 115.66γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary