6YCK

Crystal structure of GcoA T296A bound to p-vanillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Engineering a Cytochrome P450 for Demethylation of Lignin-Derived Aromatic Aldehydes.

Ellis, E.S.Hinchen, D.J.Bleem, A.Bu, L.Mallinson, S.J.B.Allen, M.D.Streit, B.R.Machovina, M.M.Doolin, Q.V.Michener, W.E.Johnson, C.W.Knott, B.C.Beckham, G.T.McGeehan, J.E.DuBois, J.L.

(2021) JACS Au 1: 252-261

  • DOI: https://doi.org/10.1021/jacsau.0c00103
  • Primary Citation of Related Structures:  
    6YCH, 6YCI, 6YCJ, 6YCK, 6YCL, 6YCM, 6YCN, 6YCO, 6YCP, 6YCT

  • PubMed Abstract: 

    Biological funneling of lignin-derived aromatic compounds is a promising approach for valorizing its catalytic depolymerization products. Industrial processes for aromatic bioconversion will require efficient enzymes for key reactions, including demethylation of O -methoxy-aryl groups, an essential and often rate-limiting step. The recently characterized GcoAB cytochrome P450 system comprises a coupled monoxygenase (GcoA) and reductase (GcoB) that catalyzes oxidative demethylation of the O- methoxy-aryl group in guaiacol. Here, we evaluate a series of engineered GcoA variants for their ability to demethylate o -and p -vanillin, which are abundant lignin depolymerization products. Two rationally designed, single amino acid substitutions, F169S and T296S, are required to convert GcoA into an efficient catalyst toward the o - and p -isomers of vanillin, respectively. Gain-of-function in each case is explained in light of an extensive series of enzyme-ligand structures, kinetic data, and molecular dynamics simulations. Using strains of Pseudomonas putida KT2440 already optimized for p -vanillin production from ferulate, we demonstrate demethylation by the T296S variant in vivo . This work expands the known aromatic O- demethylation capacity of cytochrome P450 enzymes toward important lignin-derived aromatic monomers.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Montana State University, 103 Chemistry and Biochemistry Building, PO Box 173400, Bozeman, Montana 59717, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aromatic O-demethylase, cytochrome P450 subunit409Amycolatopsis sp. ATCC 39116Mutation(s): 1 
Gene Names: gcoA
EC: 1.14.14
UniProt
Find proteins for P0DPQ7 (Amycolatopsis sp. (strain ATCC 39116 / 75iv2))
Explore P0DPQ7 
Go to UniProtKB:  P0DPQ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DPQ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
EPE
Query on EPE

Download Ideal Coordinates CCD File 
D [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
V55 (Subject of Investigation/LOI)
Query on V55

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.101α = 90
b = 105.101β = 90
c = 113.135γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P011918/1
Department of Energy (DOE, United States)United StatesDE-AC36-08GO28308

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description