PDBsum entry 1yr8

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Hydrolase PDB id
Protein chain
246 a.a. *
Waters ×18
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Pab0955 crystal structure : a gtpase in gtp bound form from abyssi
Structure: Atp(gtp)binding protein. Chain: a. Fragment: residues 1-248. Synonym: pab0955 gene product. Engineered: yes
Source: Pyrococcus abyssi. Organism_taxid: 29292. Gene: pab0955. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
2.40Å     R-factor:   0.242     R-free:   0.325
Authors: S.Gras,P.Carpentier,J.Armengaud,D.Housset
Key ref:
S.Gras et al. (2007). Structural insights into a new homodimeric self-activated GTPase family. EMBO Rep, 8, 569-575. PubMed id: 17468740 DOI: 10.1038/sj.embor.7400958
03-Feb-05     Release date:   14-Feb-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9UYR9  (Q9UYR9_PYRAB) -  GPN-loop GTPase PAB0955
248 a.a.
246 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     nucleotide binding     4 terms  


DOI no: 10.1038/sj.embor.7400958 EMBO Rep 8:569-575 (2007)
PubMed id: 17468740  
Structural insights into a new homodimeric self-activated GTPase family.
S.Gras, V.Chaumont, B.Fernandez, P.Carpentier, F.Charrier-Savournin, S.Schmitt, C.Pineau, D.Flament, A.Hecker, P.Forterre, J.Armengaud, D.Housset.
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.
  Selected figure(s)  
Figure 1.
Figure 1 Overall structure and topology of PAB0955 GPN-loop GTPase. (A) View of the PAB0955-GDP dimer. Monomer's A and B are shown in pink and light green, respectively. GDP molecules are shown as sticks coloured according to atom type (light blue for carbon, blue for nitrogen, red for oxygen, green for phosphorus). The G1, G2, G3, G4 and G5 motifs (A monomer) are shown in yellow, orange, blue, green and cyan, respectively. The two insertions I1 and I2 are depicted in fully saturated and partially saturated colours respectively. (B) Topology of PAB0955. G1–G5 boxes are shown with the same colour scheme.
Figure 3.
Figure 3 View of the PAB0955 residues stabilizing the phosphate ion in the PAB0955-PiGDP structure. Hydrogen bonds are represented as dotted lines. G1 to G5 boxes are shown with the colour scheme used in Fig 1; the GPN motif is shown in purple.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO Rep (2007, 8, 569-575) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21169697 R.Talon, R.Kahn, M.A.Durá, O.Maury, F.M.Vellieux, B.Franzetti, and E.Girard (2011).
Using lanthanoid complexes to phase large macromolecular assemblies.
  J Synchrotron Radiat, 18, 74-78.  
20855544 D.Forget, A.A.Lacombe, P.Cloutier, R.Al-Khoury, A.Bouchard, M.Lavallée-Adam, D.Faubert, C.Jeronimo, M.Blanchette, and B.Coulombe (2010).
The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II.
  Mol Cell Proteomics, 9, 2827-2839.  
21083931 S.A.Fremgen, N.S.Burke, and P.L.Hartzell (2010).
Effects of site-directed mutagenesis of mglA on motility and swarming of Myxococcus xanthus.
  BMC Microbiol, 10, 295.  
17955301 H.Namazi (2008).
Practice pearl: a novel use of botulinum toxin for unicameral bone cyst ablation.
  Ann Surg Oncol, 15, 657-658.  
18400081 J.Berthon, D.Cortez, and P.Forterre (2008).
Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation.
  Genome Biol, 9, R71.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.