9RI2 | pdb_00009ri2

Crystal structure of bacillithiol methyltransferase NmbA from Chlorobaculum tepidum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.253 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: in silico
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Literature

The methyltransferase NmbA methylates the low-molecular weight thiol bacillithiol, and displays a specific structural architecture.

Hammerstad, M.Steinvik, E.Hersleth, H.P.

(2025) Redox Biol 88: 103937-103937

  • DOI: https://doi.org/10.1016/j.redox.2025.103937
  • Primary Citation of Related Structures:  
    9RI2

  • PubMed Abstract: 

    Low-molecular-weight (LMW) thiols maintain the cellular redox balance and protect cells against reactive species, heavy metals, toxins, and antibiotics. Despite having similar metabolic functions, structurally distinct LMW thiols are widespread in nature, with bacillithiol (BSH) being the predominant LMW thiol in bacteria. The LMW thiol N-methyl-BSH (N-Me-BSH) has been identified in the green sulfur bacterium Chlorobaculum tepidum, revealing the presence of a putative S-adenosyl-l-methionine (SAM)-dependent methyltransferase (MT), NmbA, which could catalyze the final biosynthetic step of N-Me-BSH. In this study, we report biochemical evidence for NmbA's specific function as an MT of the N-atom of the BSH cysteine moiety. We also present the crystal structure of NmbA, confirming that NmbA is a Class I SAM-dependent MT, however, displaying a unique three-dimensional architecture that differs from those of other natural product MTs (NPMTs). The NmbA active site has a narrow molecular basket structure resulting from an unusual organization of the variable Cap domain, and our docking calculations suggests that it can specifically accommodate the BSH substrate. Our research provides a valuable overview of the phylogenetic distribution of N-Me-BSH in bacteria, alongside essential functional and structural insight into a new class of N-directed NPMTs. These findings contribute to the field of SAM-dependent MTs and may allow for targeting distinct bacterial defense mechanisms involving LMW thiols with potential environmental, biotechnological, and medical implications.


  • Organizational Affiliation
    • Section for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo, 0316, Norway. Electronic address: marta.hammerstad@ibv.uio.no.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyltransferase, putative
A, B
266Chlorobaculum tepidum TLSMutation(s): 0 
Gene Names: CT1040
UniProt
Find proteins for Q8KDK7 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
Explore Q8KDK7 
Go to UniProtKB:  Q8KDK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KDK7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.253 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.751α = 90
b = 55.517β = 90
c = 186.017γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Norwegian Research CouncilNorway301584

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Database references