Bifunctional tRNA modification enzyme MnmC from Escherichia coli

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli

Kitamura, A.Sengoku, T.Nishimoto, M.Yokoyama, S.Bessho, Y.

(2011) Protein Sci 

  • DOI: https://doi.org/10.1002/pro.659
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Post-transcriptional modifications of bases within the transfer RNAs (tRNA) anticodon significantly affect the decoding system. In bacteria and eukaryotes, uridines at the wobble position (U34) of some tRNAs are modified to 5-methyluridine derivatives (xm⁵U). These xm⁵U34-containing tRNAs read codons ending with A or G, whereas tRNAs with the unmodified U34 are able to read all four synonymous codons of a family box. In Escherichia coli (E.coli), the bifunctional enzyme MnmC catalyzes the two consecutive reactions that convert 5-carboxymethylaminomethyl uridine (cmnm⁵U) to 5-methylaminomethyl uridine (mnm⁵U). The C-terminal domain of MnmC (MnmC1) is responsible for the flavin adenine dinucleotide (FAD)-dependent deacetylation of cmnm⁵U to 5-aminomethyl uridine (nm⁵U), whereas the N-terminal domain (MnmC2) catalyzes the subsequent S-adenosyl-L-methionine-dependent methylation of nm⁵U, leading to the final product, mnm⁵U34. Here, we determined the crystal structure of E.coli MnmC containing FAD, at 3.0 Å resolution. The structure of the MnmC1 domain can be classified in the FAD-dependent glutathione reductase 2 structural family, including the glycine oxidase ThiO, whereas the MnmC2 domain adopts the canonical class I methyltransferase fold. A structural comparison with ThiO revealed the residues that may be involved in cmnm⁵U recognition, supporting previous mutational analyses. The catalytic sites of the two reactions are both surrounded by conserved basic residues for possible anticodon binding, and are located far away from each other, on opposite sides of the protein. These results suggest that, although the MnmC1 and MnmC2 domains are physically linked, they could catalyze the two consecutive reactions in a rather independent manner.

  • Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC
A, B, C, D, E
A, B, C, D, E, F
688Escherichia coli K-12Mutation(s): 0 
Gene Names: mnmCyfcKb2324JW5380
EC: (PDB Primary Data), 1.5 (PDB Primary Data)
Find proteins for P77182 (Escherichia coli (strain K12))
Explore P77182 
Go to UniProtKB:  P77182
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77182
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
M [auth C]
Q [auth D]
T [auth E]
G [auth A],
J [auth B],
M [auth C],
Q [auth D],
T [auth E],
V [auth F]
C27 H33 N9 O15 P2
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
K [auth B]
L [auth B]
N [auth C]
H [auth A],
I [auth A],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
U [auth E],
W [auth F]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.138α = 90
b = 243.022β = 90.42
c = 175.527γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations