5NCB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.151 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.128 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 
    0.129 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.3 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
Cytochrome P450409Amycolatopsis sp. ATCC 39116Mutation(s): 0 
Gene Names: WP_020419855
UniProt
Find proteins for A0A076MY51 (Amycolatopsis methanolica 239)
Explore A0A076MY51 
Go to UniProtKB:  A0A076MY51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A076MY51
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.151 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.128 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 0.129 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.08α = 90
b = 104.08β = 90
c = 115.754γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
CRANK2phasing

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 details

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
Department of Energy (DOE, United States)United StatesDE-AC36-08GO28308

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: 2022-03-30
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary