PDBsum entry 2oxr

Hydrolase

PDB id: 2oxr

Contents

Protein chain

246 a.a. *

Ligands

GDP

Metals

_MG

Waters ×56

* Residue conservation analysis

PDB id:

2oxr

Name:

Hydrolase

Title:

Pab0955 crystal structure : a gtpase in gdp and mg bound form from pyrococcus abyssi (after gtp hydrolysis)

Structure:

Atp(gtp)binding protein. Chain: a. Engineered: yes

Source:

Pyrococcus abyssi. Organism_taxid: 29292. Gene: pab0955. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.221 R-free: 0.324

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

Date:

21-Feb-07 Release date: 24-Apr-07

Protein chain

Q9UYR9  (GPN_PYRAB) -  GPN-loop GTPase PAB0955 from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 248 a.a.

Struc: 246 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.5.- - ?????

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.

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 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.