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PDBsum entry 3ikj
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References listed in PDB file
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Key reference
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Title
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Nucleotide binding states of subunit a of the a-Atp synthase and the implication of p-Loop switch in evolution.
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Authors
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A.Kumar,
M.S.Manimekalai,
A.M.Balakrishna,
J.Jeyakanthan,
G.Grüber.
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Ref.
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J Mol Biol, 2010,
396,
301-320.
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PubMed id
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Abstract
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The crystal structures of the nucleotide-empty (A(E)),
5'-adenylyl-beta,gamma-imidodiphosphate (A(PNP))-bound, and ADP (A(DP))-bound
forms of the catalytic A subunit of the energy producer A(1)A(O) ATP synthase
from Pyrococcus horikoshii OT3 have been solved at 2.47 A and 2.4 A resolutions.
The structures provide novel features of nucleotide binding and depict the
residues involved in the catalysis of the A subunit. In the A(E) form, the
phosphate analog SO(4)(2-) binds, via a water molecule, to the phosphate binding
loop (P-loop) residue Ser238, which is also involved in the phosphate binding of
ADP and 5'-adenylyl-beta,gamma-imidodiphosphate. Together with amino acids
Gly234 and Phe236, the serine residue stabilizes the arched P-loop conformation
of subunit A, as shown by the 2.4-A structure of the mutant protein S238A in
which the P-loop flips into a relaxed state, comparable to the one in catalytic
beta subunits of F(1)F(O) ATP synthases. Superposition of the existing P-loop
structures of ATPases emphasizes the unique P-loop in subunit A, which is also
discussed in the light of an evolutionary P-loop switch in related A(1)A(O) ATP
synthases, F(1)F(O) ATP synthases, and vacuolar ATPases and implicates diverse
catalytic mechanisms inside these biological motors.
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Secondary reference #1
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Title
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Structure of the catalytic nucleotide-Binding subunit a of a-Type ATP synthase from pyrococcus horikoshii reveals a novel domain related to the peripheral stalk.
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Authors
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Y.Maegawa,
H.Morita,
D.Iyaguchi,
M.Yao,
N.Watanabe,
I.Tanaka.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2006,
62,
483-488.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 Catalytic nucleotide-binding subunit A of Pho A-ATPase.
(a) Schematic model based on the model of Methanococcus janashii
A-ATPase (Coskun, Chaban et al., 2004[Coskun, U., Chaban, Y. L.,
Lingl, A., Muller, V., Keegstra, W., Boekema, E. J. & Gruber, G.
(2004). J. Biol. Chem. 279, 38644-38648.]). Three catalytic A
subunits are coloured grey. (b) Structure of Pho A-ATPase
catalytic nucleotide-binding subunit A. (c) Overall structure of
the catalytic nucleotide-binding subunit  of
bovine mitochondrial F-ATPase (empty form). (d) Domain II. The
direction of view is approximately horizontal to that in (b).
Eight -strands
are labelled S1-S8, respectively. (e) Archetype of the similar
structures of domain II and the biotinyl domain of acetyl-CoA
carboxylase (PDB code [82]1bdo ). The biotinylated lysine
residue is represented as a ball-and-stick model.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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