5OMS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.152 

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:  

  • 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-deri ...

    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

    Institute of Chemistry, University of Campinas, Campinas, Sao Paulo, 13083-970, Brazil.,Molecular Biophysics, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK.,Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA. jennifer.dubois1@montana.edu.,Molecular Biophysics, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK. john.mcgeehan@port.ac.uk.,Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA. houk@chem.ucla.edu.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. gregg.beckham@nrel.gov.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.,Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450
A
409Amycolatopsis sp. (strain ATCC 39116 / 75iv2)Mutation(s): 0 
Find proteins for A0A3B6UEE9 (Amycolatopsis sp. (strain ATCC 39116 / 75iv2))
Go to UniProtKB:  A0A3B6UEE9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
261
Query on 261

Download SDF File 
Download CCD File 
A
2-ethoxyphenol
C8 H10 O2
MOEFFSWKSMRFRQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.152 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.280α = 90.00
b = 104.280β = 90.00
c = 114.620γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
xia2data reduction
PHENIXrefinement
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references