2GJA

Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and NH4+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 1.2 of the entry. See complete history


Literature

Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element.

Scrima, A.Wittinghofer, A.

(2006) EMBO J 25: 2940-2951

  • DOI: 10.1038/sj.emboj.7601171
  • Primary Citation of Related Structures:  
    2GJ8, 2GJ9, 2GJA

  • PubMed Abstract: 
  • MnmE, a Guanine nucleotide-binding protein conserved between bacteria and man, is involved in the modification of tRNAs. Here we provide biochemical and X-ray structural evidence for a new GTP-hydrolysis mechanism, where the G-domains of MnmE dimerise in a potassium-dependent manner and induce GTP hydrolysis ...

    MnmE, a Guanine nucleotide-binding protein conserved between bacteria and man, is involved in the modification of tRNAs. Here we provide biochemical and X-ray structural evidence for a new GTP-hydrolysis mechanism, where the G-domains of MnmE dimerise in a potassium-dependent manner and induce GTP hydrolysis. The structure in the presence of GDP-AlFx and potassium shows how juxtaposition of the subunits induces a conformational change around the nucleotide which reorients the catalytic machinery. A critical glutamate is positioned such as to stabilise or activate the attacking water. Potassium provides a positive charge into the catalytic site in a position analogous to the arginine finger in the Ras-RasGAP system. Mutational studies show that potassium-dependent dimerisation and GTP hydrolysis can be uncoupled and that interaction between the G-domains is a prerequisite for subsequent phosphoryl transfer. We propose a model for the juxtaposition of G-domains in the full-length protein and how it induces conformational changes in the putative tRNA-modification centre.


    Organizational Affiliation

    Max-Planck-Institut für Molekulare Physiologie, Dortmund, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA modification GTPase trmEA, B172Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: trmEmnmEthdF
EC: 3.6
UniProt
Find proteins for P25522 (Escherichia coli (strain K12))
Explore P25522 
Go to UniProtKB:  P25522
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.28α = 90
b = 90.65β = 90
c = 138.47γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance