8C9V | pdb_00008c9v

O-methyltransferase from Desulfuromonas acetoxidans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.173 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural Characterization and Extended Substrate Scope Analysis of Two Mg 2+ -Dependent O-Methyltransferases from Bacteria.

Sokolova, N.Zhang, L.Deravi, S.Oerlemans, R.Groves, M.R.Haslinger, K.

(2023) Chembiochem 24: e202300076-e202300076

  • DOI: https://doi.org/10.1002/cbic.202300076
  • Primary Citation Related Structures: 
    8C9S, 8C9T, 8C9V

  • PubMed Abstract: 

    Oxygen-directed methylation is a ubiquitous tailoring reaction in natural product pathways catalysed by O-methyltransferases (OMTs). Promiscuous OMT biocatalysts are thus a valuable asset in the toolkit for sustainable synthesis and optimization of known bioactive scaffolds for drug development. Here, we characterized the enzymatic properties and substrate scope of two bacterial OMTs from Desulforomonas acetoxidans and Streptomyces avermitilis and determined their crystal structures. Both OMTs methylated a wide range of catechol-like substrates, including flavonoids, coumarins, hydroxybenzoic acids, and their respective aldehydes, an anthraquinone and an indole. One enzyme also accepted a steroid. The product range included pharmaceutically relevant compounds such as (iso)fraxidin, iso(scopoletin), chrysoeriol, alizarin 1-methyl ether, and 2-methoxyestradiol. Interestingly, certain non-catechol flavonoids and hydroxybenzoic acids were also methylated. This study expands the knowledge on substrate preference and structural diversity of bacterial catechol OMTs and paves the way for their use in (combinatorial) pathway engineering.


  • Organizational Affiliation
    • Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9731AV, Groningen, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 22.67 kDa 
  • Atom Count: 1,549 
  • Modeled Residue Count: 187 
  • Deposited Residue Count: 203 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
O-methyltransferase, family 3203Desulfuromonas acetoxidans DSM 684Mutation(s): 0 
Gene Names: Dace_1119
UniProt
Find proteins for Q1JXV1 (Desulfuromonas acetoxidans (strain DSM 684 / 11070))
Explore Q1JXV1 
Go to UniProtKB:  Q1JXV1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1JXV1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.173 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.791α = 90
b = 44.791β = 90
c = 204.919γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
Aimlessdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union893122

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Refinement description