9BXM | pdb_00009bxm

OvoM from Sulfuricurvum sp. isolate STB_99, a SAM-dependent N-methyltransferase involved in ovothiol biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and functional analysis of SAM-dependent N-methyltransferases involved in ovoselenol and ovothiol biosynthesis.

Ireland, K.A.Kayrouz, C.M.Abbott, M.L.Seyedsayamdost, M.R.Davis, K.M.

(2025) Structure 33: 528-538.e5

  • DOI: https://doi.org/10.1016/j.str.2024.12.020
  • Primary Citation of Related Structures:  
    9BXH, 9BXJ, 9BXK, 9BXL, 9BXM, 9BXN

  • PubMed Abstract: 

    Thio/selenoimidazole Nπ-methyltransferases are an emerging family of enzymes catalyzing the final step in the production of the S/Se-containing histidine-derived antioxidants ovothiol and ovoselenol. These enzymes, prevalent in prokaryotes, show minimal sequence similarity to other methyltransferases, and the structural determinants of their reactivities remain poorly understood. Herein, we report ligand-bound crystal structures of OvsM from the ovoselenol pathway as well as a member of a previously unknown clade of standalone ovothiol-biosynthetic Nπ-methyltransferases, which we have designated OvoM. Unlike previously reported ovothiol methyltransferases, which are fused as a C-terminal domain to the sulfoxide synthase OvoA, OvoMs function independently. Comparative structural analyses reveal conserved, ligand-induced conformational changes, suggesting similar behavior in dual-domain OvoA enzymes. Mutagenesis supports a model where OvoA domain rearrangement facilitates substrate recognition via a critical Tyr residue in the domain linker. Biochemical studies identify an essential active-site Asp, likely serving as a catalytic base in the S N 2-like nucleophilic substitution reaction.


  • Organizational Affiliation
    • Department of Chemistry, Emory University, Atlanta, GA 30322, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-thiohistidine N-methyltransferase OvoM
A, B
273Sulfuricurvum sp.Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.16α = 90
b = 92.215β = 90
c = 95.999γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1937971
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM147557

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Database references
  • Version 1.2: 2025-03-19
    Changes: Database references