9YCE | pdb_00009yce

Active site of MtgB, a glycine betaine methyltransferase from the MttB superfamily


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.216 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Delineation of the active site of MtgB, a cobalamin-dependent glycine betaine methyltransferase.

Picking, J.Li, Y.Ticak, T.Ferguson, D.J.Hao, B.Krzycki, J.A.

(2026) J Biological Chem 302: 111216-111216

  • DOI: https://doi.org/10.1016/j.jbc.2026.111216
  • Primary Citation of Related Structures:  
    9YCE

  • PubMed Abstract: 

    The MttB superfamily member MtgB catalyzes the methylation of a cognate corrinoid protein with glycine betaine, and representatives have been described from both bacteria and archaea. Here, we focused on MtgB from Desulfitobacterium hafniense, a protein for which a crystal structure had been previously obtained. We employed different programs to predict the binding of glycine betaine and identified a consensus binding site. The modelled binding site consisted of two aromatic residues, Y97 and F356, which are both proposed to interact with the quaternary amine portion of glycine betaine via pi:cation interactions. Additionally, two basic residues, H348 and R312, were proposed to interact with the carboxylate group. We carried out site-directed substitutions and subsequently tested the necessity of these residues for glycine betaine:cob(I)alamin methyltransferase activity. These experiments supported a role in catalysis for each residue, presumably in the placement of glycine betaine at the proper position for nucleophilic attack by the Co(I) ion of cobalamin. Subsequently, the structure of the glycine betaine-bound enzyme was obtained, confirming the interaction of these residues with glycine betaine. Other MttB superfamily members with specificity for different quaternary amines were modeled and compared with the glycine betaine-bound structure of MtgB. The nitrogen of each quaternary amine was brought within an average value of 1.8 Å to each other, suggesting that members of the superfamily bring their methyl groups into nearly the same space within the TIM barrel prior to methyl group transfer to cob(I)alamin.


  • Organizational Affiliation
    • Department of Microbiology, The Ohio State University, Columbus, Ohio, USA; The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine betaine methyltransferase
A, B
477Desulfitobacterium hafniense Y51Mutation(s): 0 
Gene Names: mtgBDSY3156
EC: 2.1.1.376
UniProt
Find proteins for Q24SP7 (Desulfitobacterium hafniense (strain Y51))
Explore Q24SP7 
Go to UniProtKB:  Q24SP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ24SP7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.216 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.465α = 90
b = 123.465β = 90
c = 123.531γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata scaling
autoPROCdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135592

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-11
    Type: Initial release