6HQR

Crystal structure of GcoA F169H bound to syringol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

  • 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 ...

    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; houk@chem.ucla.edu gregg.beckham@nrel.gov john.mcgeehan@port.ac.uk jennifer.dubois1@montana.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450A407Amycolatopsis sp. ATCC 39116Mutation(s): 1 
Gene Names: AMETH_3834gcoA
EC: 1.14.14
UniProt
Find proteins for P0DPQ7 (Amycolatopsis sp. (strain ATCC 39116 / 75iv2))
Explore P0DPQ7 
Go to UniProtKB:  P0DPQ7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
3DM (Subject of Investigation/LOI)
Query on 3DM

Download Ideal Coordinates CCD File 
C [auth A]2,6-dimethoxyphenol
C8 H10 O3
KLIDCXVFHGNTTM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.104α = 90
b = 102.104β = 90
c = 109.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

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 (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