1YRB

PAB0955 crystal structure : a GTPase in GDP and Mg bound form from Pyrococcus abyssi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural insights into a new homodimeric self-activated GTPase family.

Gras, S.Chaumont, V.Fernandez, B.Carpentier, P.Charrier-Savournin, F.Schmitt, S.Pineau, C.Flament, D.Hecker, A.Forterre, P.Armengaud, J.Housset, D.

(2007) Embo Rep. 8: 569-575

  • DOI: 10.1038/sj.embor.7400958
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human XAB1/MBDin GTPase and its close homologues form one of the ten phylogenetically distinct families of the SIMIBI (after signal recognition particle, MinD and BioD) class of phosphate-binding loop NTPases. The genomic context and the partners ...

    The human XAB1/MBDin GTPase and its close homologues form one of the ten phylogenetically distinct families of the SIMIBI (after signal recognition particle, MinD and BioD) class of phosphate-binding loop NTPases. The genomic context and the partners identified for the archaeal and eukaryotic homologues indicate that they are involved in genome maintenance--DNA repair or replication. The crystal structure of PAB0955 from Pyrococcus abyssi shows that, unlike other SIMIBI class G proteins, these highly conserved GTPases are homodimeric, regardless of the presence of nucleotides. The nucleotide-binding site of PAB0955 is rather rigid and its conformation is closest to that of the activated SRP G domain. One insertion to the G domain bears a strictly conserved GPN motif, which is part of the catalytic site of the other monomer and stabilizes the phosphate ion formed. Owing to this unique functional feature, we propose to call this family as GPN-loop GTPase.


    Related Citations: 
    • Expression, purification, crystallization and preliminary crystallographic analysis of the PAB0955 gene product
      Gras, S.,Fernandez, B.,Chaumont, V.,Carpentier, P.,Armengaud, J.,Housset, D.
      (2005) Acta Crystallogr.,Sect.F 61: 208


    Organizational Affiliation

    Laboratoire de Cristallographie et Cristallogénèse des Protéines, Institut de Biologie Structurale J.-P. Ebel, CEA-CNRS-UJF, UMR 5075, 41, Rue Jules Horowitz, F-38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP(GTP)binding protein
A, B
262Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
EC: 3.6.5.-
Find proteins for Q9UYR9 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9UYR9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.470α = 90.00
b = 85.210β = 94.61
c = 60.570γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ProDCdata collection
AMoREphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-11-12
    Type: Structure summary
  • Version 1.4: 2017-10-11
    Type: Refinement description