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PDBsum entry 1yrb
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References listed in PDB file
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Key reference
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Title
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Structural insights into a new homodimeric self-Activated gtpase family.
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Authors
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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.
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Ref.
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EMBO Rep, 2007,
8,
569-575.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO Rep
(2007,
8,
569-575)
copyright 2007.
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Secondary reference #1
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Title
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Expression, Purification, Crystallization and preliminary crystallographic analysis of the pab0955 gene product
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Authors
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S.Gras,
B.Fernandez,
V.Chaumont,
P.Carpentier,
J.Armengaud,
D.Housset.
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Ref.
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acta crystallogr ,sect f, 2005,
61,
208.
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