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PDBsum entry 1t9h
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References listed in PDB file
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Key reference
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Title
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The crystal structure of yloq, A circularly permuted gtpase essential for bacillus subtilis viability.
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Authors
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V.M.Levdikov,
E.V.Blagova,
J.A.Brannigan,
L.Cladière,
A.A.Antson,
M.N.Isupov,
S.J.Séror,
A.J.Wilkinson.
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Ref.
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J Mol Biol, 2004,
340,
767-782.
[DOI no: ]
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PubMed id
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Abstract
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yloQ is one of 11 essential genes in Bacillus subtilis with unknown roles in the
physiology of the cell. It encodes a polypeptide of 298 residues with motifs
characteristic of GTPases. As a contribution to elucidating its indispensable
cellular function, we have solved the crystal structure of YloQ to 1.6 A
spacing, revealing a three-domain organisation. At the heart of the molecule is
the putative GTPase domain, which exhibits a classical alpha/beta
nucleotide-binding fold with a topology very similar to that of Ras and Era.
However, as anticipated from the order in which the conserved G protein motifs
appear in the sequence, the GTPase domain fold in YloQ is circularly permuted
with respect to the classical GTPases. The nucleotide-binding pocket in YloQ is
unoccupied, and analysis of the phosphate-binding (P) loop indicates that
conformational changes in this region would be needed to accommodate GTP. The
GTPase domain is flanked at its N terminus by a beta-barrel domain with an
oligonucleotide/oligosaccharide-binding (OB) fold, and at its C terminus by an
alpha-helical domain containing a coordinated zinc ion. This combination of
protein modules is unique to YloQ and its orthologues. Sequence comparisons
reveal a clustering of conserved basic and aromatic residues on one face of the
OB domain, perhaps pointing to a role for YloQ in nucleic acid binding. The zinc
ion in the alpha-helical domain is coordinated by three cysteine residues and a
histidine residue in a novel ligand organisation. The juxtaposition of the
switch I and switch II regions of the G domain and the OB and zinc-binding
domains suggests that chemical events at the GTPase active site may be
transduced into relative movements of these domains. The pattern of conserved
residues and electrostatic surface potential calculations suggest that the OB
and/or Zn-binding domains participate in nucleic acid binding consistent with a
possible role for YloQ at some stage during mRNA translation.
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Figure 4.
Figure 4. Ribbon tracing of the GTPase domain of YloQ (A)
and Era (B). The ribbons are colour-ramped from the N terminus
(blue) to the C terminus (red). The secondary structure elements
are labelled. In YloQ, the break in the ribbon connecting a4 to
b12 is caused by residues 187-205 being disordered and absent
from the model. Topology diagrams of YloQ (C) and Era (D)
illustrating the circular permutation of the GTPase domain.
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Figure 5.
Figure 5. Superimposition of the GTPase domains of YloQ and
the Ras-GDPNP complex (PDB accession, 1LF0) as a stereo view.
The ribbon tracing of YloQ is presented in cyan, that for Ras is
in yellow. The guanine nucleotide bound in Ras is displayed in
ball-and-stick format in magenta. The broken line indicates the
disordered region in the YloQ molecule. The G1 (P-loop), G2
(Switch I), G3 (Switch II) and G4 (guanine specificity motif)
segments of YloQ are coloured red. The structures were
overlapped initially in the program MOLREP,[35.] and
subsequently adjusted manually to emphasise similarities and
differences in the P-loop region.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
340,
767-782)
copyright 2004.
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Secondary reference #1
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Title
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Crystallization of yloq, A gtpase of unknown function essential for bacillus subtilis viability.
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Authors
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L.Cladière,
E.Blagova,
V.M.Levdikov,
J.A.Brannigan,
S.J.Séror,
A.J.Wilkinson.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2004,
60,
329-330.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 Crystals of YloQ grown from (a) 0.1 M HEPES pH 7.5,
0.2 M calcium acetate and 10-14% polyethylene glycol 5000 and
(b) 0.1 M HEPES pH 7.5, 0.8 M sodium formate and 22%
polyethylene glycol 2000. The width of these panels corresponds
to [33]~ 1 mm.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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