8C9S

Catechol O-methyltransferase from Streptomyces avermitilis in complex with SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.162 

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Ligand Structure Quality Assessment 


This is version 1.1 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative O-methyltransferase
A, B
232Streptomyces avermitilis MA-4680 = NBRC 14893Mutation(s): 0 
Gene Names: SAVERM_5837
UniProt
Find proteins for Q82B68 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680))
Explore Q82B68 
Go to UniProtKB:  Q82B68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82B68
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.398α = 90
b = 41.596β = 96.564
c = 104.207γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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