5OMR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted V55Click on this verticalbar to view details

This is version 1.2 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GcoA409Amycolatopsis sp. ATCC 39116Mutation(s): 0 
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
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
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted V55Click on this verticalbar to view details

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