Crystal structure of MnmM from S. aureus in apo state (1.44 A)

Experimental Data Snapshot

  • Resolution: 1.44 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification.

Cho, G.Lee, J.Kim, J.

(2023) Nucleic Acids Res 51: 1971-1983

  • DOI: https://doi.org/10.1093/nar/gkad048
  • Primary Citation of Related Structures:  
    8H0S, 8H0T, 8H1A, 8H1B, 8H27

  • PubMed Abstract: 

    The uridine at the 34th position of tRNA, which is able to base pair with the 3'-end codon on mRNA, is usually modified to influence many aspects of decoding properties during translation. Derivatives of 5-methyluridine (xm5U), which include methylaminomethyl (mnm-) or carboxymethylaminomethyl (cmnm-) groups at C5 of uracil base, are widely conserved at the 34th position of many prokaryotic tRNAs. In Gram-negative bacteria such as Escherichia coli, a bifunctional MnmC is involved in the last two reactions of the biosynthesis of mnm5(s2)U, in which the enzyme first converts cmnm5(s2)U to 5-aminomethyl-(2-thio)uridine (nm5(s2)U) and subsequently installs the methyl group to complete the formation of mnm5(s2)U. Although mnm5s2U has been identified in tRNAs of Gram-positive bacteria and plants as well, their genomes do not contain an mnmC ortholog and the gene(s) responsible for this modification is unknown. We discovered that MnmM, previously known as YtqB, is the methyltransferase that converts nm5s2U to mnm5s2U in Bacillus subtilis through comparative genomics, gene complementation experiments, and in vitro assays. Furthermore, we determined X-ray crystal structures of MnmM complexed with anticodon stem loop of tRNAGln. The structures provide the molecular basis underlying the importance of U33-nm5s2U34-U35 as the key determinant for the specificity of MnmM.

  • Organizational Affiliation

    Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA methylase YtqB
A, B
195Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: SAOUHSC_01878
Find proteins for Q2FXG9 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXG9 
Go to UniProtKB:  Q2FXG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FXG9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.44 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.494α = 90
b = 63.91β = 90
c = 135.044γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
STARANISOdata scaling
XDSdata reduction
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description