6YCK | pdb_00006yck

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 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6YCK

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 46.43 kDa 
  • Atom Count: 3,641 
  • Modeled Residue Count: 403 
  • Deposited Residue Count: 409 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.181 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
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



Ligand Structure Quality Assessment 


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