3PVC

Crystal structure of apo MnmC from Yersinia Pestis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

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This is version 1.4 of the entry. See complete history. 


Literature

Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC.

Kim, J., Almo, S.C.

(2013) BMC Struct Biol 13: 5-5

  • DOI: https://doi.org/10.1186/1472-6807-13-5
  • Primary Citation of Related Structures:  
    3PS9, 3PVC, 3SGL

  • PubMed Abstract: 

    Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the biosynthetic pathway responsible for this post-transcriptional modification, the bifunctional enzyme MnmC catalyzes the conversion of its hypermodified substrate carboxymethylaminomethyl uridine (cmnm5U34) to mnm5U34. MnmC catalyzes the flavin adenine dinucleotide (FAD)-dependent oxidative cleavage of carboxymethyl group from cmnm5U34 via an imine intermediate to generate aminomethyl uridine (nm5U34), which is subsequently methylated by S-adenosyl-L-methionine (SAM) to yield methylaminomethyl uridine (mnm5U34).

    • Organizational Affiliation: 

    Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA. jukim@aecom.yu.edu


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC689Yersinia pestisMutation(s): 0 
Gene Names: mnmC, y1590, YPO2756, YP_2407
EC: 2.1.1 (PDB Primary Data), 1.5 (PDB Primary Data)
UniProt
Find proteins for Q8ZD36 (Yersinia pestis)
Explore Q8ZD36 
Go to UniProtKB:  Q8ZD36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZD36
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.146α = 90
b = 59.566β = 99.57
c = 99.63γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-17
    Changes: Structure summary
  • Version 1.3: 2011-11-16
    Changes: Structure summary
  • Version 1.4: 2013-12-25
    Changes: Database references