5NCB

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

• PDB DOI:  https://doi.org/10.2210/pdb5NCB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amycolatopsis sp. ATCC 39116
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-03 Released: 2018-07-04 
• Deposition Author(s): Mallinson, S.J.B., Johnson, C.W., Neidle, E.L., Beckham, G.T., McGeehan, J.E.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council, Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.151 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 

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

• PubMed: 29950589 
• DOI: https://doi.org/10.1038/s41467-018-04878-2
• Primary Citation of Related Structures:  
  5NCB, 5OGX, 5OMR, 5OMS, 5OMU


• 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-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.

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Organizational Affiliation: 

Molecular Biophysics, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 46.57 kDa 
• Atom Count: 3,548 
• Modelled Residue Count: 403 
• Deposited Residue Count: 409 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	409	Amycolatopsis sp. ATCC 39116	Mutation(s): 0  Gene Names: WP_020419855
UniProt
Find proteins for A0A076MY51 (Amycolatopsis methanolica 239) Explore A0A076MY51  Go to UniProtKB:  A0A076MY51

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
JZ3	C [auth A]	Guaiacol C7 H8 O2 LHGVFZTZFXWLCP-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.151 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.08	α = 90
b = 104.08	β = 90
c = 115.754	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-04 
Deposition Author(s): Mallinson, S.J.B., Johnson, C.W., Neidle, E.L., Beckham, G.T., McGeehan, J.E.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/P0119818/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/L001926/1
Department of Energy (DOE, United States)	United States	DE-AC36-08GO28308

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2018-07-11
  Changes: Data collection, Database references
• Version 1.2: 2022-03-30
  Changes: Author supporting evidence, Database references, Derived calculations