Crystal structure of GcoA F169V bound to guaiacol

Experimental Data Snapshot

  • Resolution: 1.62 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Enabling microbial syringol conversion through structure-guided protein engineering.

Machovina, M.M.Mallinson, S.J.B.Knott, B.C.Meyers, A.W.Garcia-Borras, M.Bu, L.Gado, J.E.Oliver, A.Schmidt, G.P.Hinchen, D.J.Crowley, M.F.Johnson, C.W.Neidle, E.L.Payne, C.M.Houk, K.N.Beckham, G.T.McGeehan, J.E.DuBois, J.L.

(2019) Proc Natl Acad Sci U S A 116: 13970-13976

  • DOI: https://doi.org/10.1073/pnas.1820001116
  • Primary Citation of Related Structures:  
    6HQK, 6HQL, 6HQM, 6HQN, 6HQO, 6HQP, 6HQQ, 6HQR, 6HQS, 6HQT

  • PubMed Abstract: 

    Microbial conversion of aromatic compounds is an emerging and promising strategy for valorization of the plant biopolymer lignin. A critical and often rate-limiting reaction in aromatic catabolism is O -aryl-demethylation of the abundant aromatic methoxy groups in lignin to form diols, which enables subsequent oxidative aromatic ring-opening. Recently, a cytochrome P450 system, GcoAB, was discovered to demethylate guaiacol (2-methoxyphenol), which can be produced from coniferyl alcohol-derived lignin, to form catechol. However, native GcoAB has minimal ability to demethylate syringol (2,6-dimethoxyphenol), the analogous compound that can be produced from sinapyl alcohol-derived lignin. Despite the abundance of sinapyl alcohol-based lignin in plants, no pathway for syringol catabolism has been reported to date. Here we used structure-guided protein engineering to enable microbial syringol utilization with GcoAB. Specifically, a phenylalanine residue (GcoA-F169) interferes with the binding of syringol in the active site, and on mutation to smaller amino acids, efficient syringol O -demethylation is achieved. Crystallography indicates that syringol adopts a productive binding pose in the variant, which molecular dynamics simulations trace to the elimination of steric clash between the highly flexible side chain of GcoA-F169 and the additional methoxy group of syringol. Finally, we demonstrate in vivo syringol turnover in Pseudomonas putida KT2440 with the GcoA-F169A variant. Taken together, our findings highlight the significant potential and plasticity of cytochrome P450 aromatic O -demethylases in the biological conversion of lignin-derived aromatic compounds.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450407Amycolatopsis sp. ATCC 39116Mutation(s): 1 
Gene Names: AMETH_3834
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
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.62 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.803α = 90
b = 103.803β = 90
c = 115.778γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P011918/1
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: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.3: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Refinement description