2HJG

The crystal structure of the B. subtilis YphC GTPase in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The essential GTPase YphC displays a major domain rearrangement associated with nucleotide binding.

Muench, S.P.Xu, L.Sedelnikova, S.E.Rice, D.W.

(2006) Proc.Natl.Acad.Sci.Usa 103: 12359-12364

  • DOI: 10.1073/pnas.0602585103

  • PubMed Abstract: 
  • The structure of a Bacillus subtilis YphC/GDP complex shows that it contains two GTPase domains that pack against a central domain whose fold resembles that of an RNA binding KH-domain. Comparisons of this structure to that of a homologue in Thermoto ...

    The structure of a Bacillus subtilis YphC/GDP complex shows that it contains two GTPase domains that pack against a central domain whose fold resembles that of an RNA binding KH-domain. Comparisons of this structure to that of a homologue in Thermotoga maritima reveals a dramatic rearrangement in the position of the N-terminal GTPase domain with a shift of up to 60 A and the formation of a totally different interface to the central domain. This rearrangement appears to be triggered by conformational changes of the switch II region in this domain in response to nucleotide binding. Modeling studies suggest that this motion represents transitions between the "on" and "off" states of the GTPase, the effect of which is to alternately expose and bury a positively charged face of the central domain that we suggest is involved in RNA recognition as part of the possible role of this enzyme in ribosome binding.


    Related Citations: 
    • Cloning, purification and preliminary crystallographic analysis of the Bacillus subtilis GTPase YphC-GDP complex.
      Xu, L.,Muench, S.P.,Roujeinikova, A.,Sedelnikova, S.E.,Rice, D.W.
      (2006) Acta Crystallogr.,Sect.F 62: 435


    Organizational Affiliation

    Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP-binding protein engA
A
436Bacillus subtilis (strain 168)Gene Names: der (engA, yphC)
Find proteins for P50743 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P50743
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.711α = 90.00
b = 65.045β = 90.00
c = 110.610γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Structure summary