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Contents |
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487 a.a.
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467 a.a.
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122 a.a.
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* Residue conservation analysis
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PDB id:
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Atp phosphorylase
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Title:
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Bovine mitochondrial f1-atpase inhibited by mg2+adp and aluminium fluoride
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Structure:
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Bovine mitochondrial f1-atpase. Chain: a, b, c. Synonym: atp synthase alpha chain heart isoform. Bovine mitochondrial f1-atpase. Chain: d, e, f. Synonym: atp synthase beta chain. Bovine mitochondrial f1-atpase. Chain: g. Synonym: atp synthase gamma chain.
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Source:
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Bos taurus. Bovine. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Organelle: mitochondrion. Organelle: mitochondrion
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Biol. unit:
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Heptamer (from
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Resolution:
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2.50Å
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R-factor:
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0.218
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R-free:
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0.282
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Authors:
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K.Braig,R.I.Menz,M.G.Montgomery,A.G.W.Leslie,J.E.Walker
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Key ref:
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K.Braig
et al.
(2000).
Structure of bovine mitochondrial F(1)-ATPase inhibited by Mg(2+) ADP and aluminium fluoride.
Structure,
8,
567-573.
PubMed id:
DOI:
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Date:
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10-May-00
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Release date:
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28-Jun-00
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PROCHECK
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Headers
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References
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P19483
(ATPA_BOVIN) -
ATP synthase subunit alpha, mitochondrial from Bos taurus
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Seq:
Struc:
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553 a.a.
487 a.a.*
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Enzyme class 1:
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Chains A, B, C, G:
E.C.3.6.1.34
- Transferred entry: 7.1.2.2.
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Enzyme class 2:
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Chains D, E, F:
E.C.7.1.2.2
- H(+)-transporting two-sector ATPase.
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Reaction:
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ATP + H2O + 4 H+(in) = ADP + phosphate + 5 H+(out)
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ATP
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+
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H2O
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+
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4
×
H(+)(in)
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=
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ADP
Bound ligand (Het Group name = )
corresponds exactly
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+
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phosphate
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+
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5
×
H(+)(out)
Bound ligand (Het Group name = )
corresponds exactly
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Structure
8:567-573
(2000)
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PubMed id:
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Structure of bovine mitochondrial F(1)-ATPase inhibited by Mg(2+) ADP and aluminium fluoride.
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K.Braig,
R.I.Menz,
M.G.Montgomery,
A.G.Leslie,
J.E.Walker.
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ABSTRACT
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BACKGROUND: The globular domain of the membrane-associated F(1)F(o)-ATP synthase
complex can be detached intact as a water-soluble fragment known as F(1)-ATPase.
It consists of five different subunits, alpha, beta, gamma, delta and epsilon,
assembled with the stoichiometry 3:3:1:1:1. In the crystal structure of bovine
F(1)-ATPase determined previously at 2.8 A resolution, the three catalytic beta
subunits and the three noncatalytic alpha subunits are arranged alternately
around a central alpha-helical coiled coil in the gamma subunit. In the
crystals, the catalytic sites have different nucleotide occupancies. One
contains the triphosphate form of the nucleotide, the second contains the
diphosphate, and the third is unoccupied. Fluoroaluminate complexes have been
shown to mimic the transition state in several ATP and GTP hydrolases. In order
to understand more about its catalytic mechanism, F(1)-ATPase was inhibited with
Mg(2+)ADP and aluminium fluoride and the structure of the inhibited complex was
determined by X-ray crystallography. RESULTS: The structure of bovine
F(1)-ATPase inhibited with Mg(2+)ADP and aluminium fluoride determined at 2.5 A
resolution differs little from the original structure with bound AMP-PNP and
ADP. The nucleotide occupancies of the alpha and beta subunits are unchanged
except that both aluminium trifluoride and Mg(2+)ADP are bound in the
nucleotide-binding site of the beta(DP) subunit. The presence of aluminium
fluoride is accompanied by only minor adjustments in the surrounding protein.
CONCLUSIONS: The structure appears to mimic a possible transition state. The
coordination of the aluminofluoride group has many features in common with other
aluminofluoride-NTP hydrolase complexes. Apparently, once nucleotide is bound to
the catalytic beta subunit, no additional major structural changes are required
for catalysis to occur.
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Selected figure(s)
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Figure 4.
Figure 4. Location of ADP and fluoroaluminate in the
a[DP]/b[DP] subunit interface. ADP, AlF[3] and the sidechains of
bLys162, bGlu188 (largely hidden), bArg189 and aArg373 are shown
in ball-and-stick representation, using the same atom-colouring
scheme as in Figure 1. The figure was produced using BOBSCRIPT
[32].
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2000,
8,
567-573)
copyright 2000.
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Figure was
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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I.G.Muñoz,
H.Yébenes,
M.Zhou,
P.Mesa,
M.Serna,
A.Y.Park,
E.Bragado-Nilsson,
A.Beloso,
G.de Cárcer,
M.Malumbres,
C.V.Robinson,
J.M.Valpuesta,
and
G.Montoya
(2011).
Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin.
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Nat Struct Mol Biol,
18,
14-19.
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PDB code:
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K.Okazaki,
and
S.Takada
(2011).
Structural Comparison of F(1)-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations.
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Structure,
19,
588-598.
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R.Watanabe,
R.Iino,
and
H.Noji
(2010).
Phosphate release in F1-ATPase catalytic cycle follows ADP release.
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Nat Chem Biol,
6,
814-820.
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|
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Y.Ito,
and
M.Ikeguchi
(2010).
Structural fluctuation and concerted motions in F(1)-ATPase: A molecular dynamics study.
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J Comput Chem,
31,
2175-2185.
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K.H.Nielsen,
H.Chamieh,
C.B.Andersen,
F.Fredslund,
K.Hamborg,
H.Le Hir,
and
G.R.Andersen
(2009).
Mechanism of ATP turnover inhibition in the EJC.
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RNA,
15,
67-75.
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PDB code:
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W.Li,
L.E.Brudecki,
A.E.Senior,
and
Z.Ahmad
(2009).
Role of {alpha}-Subunit VISIT-DG Sequence Residues Ser-347 and Gly-351 in the Catalytic Sites of Escherichia coli ATP Synthase.
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J Biol Chem,
284,
10747-10754.
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H.Sielaff,
H.Rennekamp,
S.Engelbrecht,
and
W.Junge
(2008).
Functional halt positions of rotary FOF1-ATPase correlated with crystal structures.
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Biophys J,
95,
4979-4987.
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J.A.Scanlon,
M.K.Al-Shawi,
and
R.K.Nakamoto
(2008).
A rotor-stator cross-link in the F1-ATPase blocks the rate-limiting step of rotational catalysis.
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J Biol Chem,
283,
26228-26240.
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M.Nakanishi-Matsui,
and
M.Futai
(2008).
Stochastic rotational catalysis of proton pumping F-ATPase.
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Philos Trans R Soc Lond B Biol Sci,
363,
2135-2142.
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N.D.Thomsen,
and
J.M.Berger
(2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
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Mol Microbiol,
69,
1071-1090.
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R.K.Nakamoto,
J.A.Baylis Scanlon,
and
M.K.Al-Shawi
(2008).
The rotary mechanism of the ATP synthase.
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Arch Biochem Biophys,
476,
43-50.
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S.Hong,
and
P.L.Pedersen
(2008).
ATP synthase and the actions of inhibitors utilized to study its roles in human health, disease, and other scientific areas.
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Microbiol Mol Biol Rev,
72,
590.
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T.Masaike,
F.Koyama-Horibe,
K.Oiwa,
M.Yoshida,
and
T.Nishizaka
(2008).
Cooperative three-step motions in catalytic subunits of F(1)-ATPase correlate with 80 degrees and 40 degrees substep rotations.
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Nat Struct Mol Biol,
15,
1326-1333.
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A.Stocker,
S.Keis,
J.Vonck,
G.M.Cook,
and
P.Dimroth
(2007).
The structural basis for unidirectional rotation of thermoalkaliphilic F1-ATPase.
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Structure,
15,
904-914.
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PDB code:
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B.A.Feniouk,
A.Rebecchi,
D.Giovannini,
S.Anefors,
A.Y.Mulkidjanian,
W.Junge,
P.Turina,
and
B.A.Melandri
(2007).
Met23Lys mutation in subunit gamma of F(O)F(1)-ATP synthase from Rhodobacter capsulatus impairs the activation of ATP hydrolysis by protonmotive force.
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Biochim Biophys Acta,
1767,
1319-1330.
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M.W.Bowler,
M.G.Montgomery,
A.G.Leslie,
and
J.E.Walker
(2007).
Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 A resolution.
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J Biol Chem,
282,
14238-14242.
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PDB code:
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O.Y.Dmitriev,
and
R.H.Fillingame
(2007).
The rigid connecting loop stabilizes hairpin folding of the two helices of the ATP synthase subunit c.
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Protein Sci,
16,
2118-2122.
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M.W.Bowler,
M.G.Montgomery,
A.G.Leslie,
and
J.E.Walker
(2006).
Reproducible improvements in order and diffraction limit of crystals of bovine mitochondrial F(1)-ATPase by controlled dehydration.
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Acta Crystallogr D Biol Crystallogr,
62,
991-995.
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E.Skordalakes,
A.P.Brogan,
B.S.Park,
H.Kohn,
and
J.M.Berger
(2005).
Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin.
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Structure,
13,
99.
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PDB codes:
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R.Iino,
T.Murakami,
S.Iizuka,
Y.Kato-Yamada,
T.Suzuki,
and
M.Yoshida
(2005).
Real-time monitoring of conformational dynamics of the epsilon subunit in F1-ATPase.
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J Biol Chem,
280,
40130-40134.
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Z.Ahmad,
and
A.E.Senior
(2005).
Modulation of charge in the phosphate binding site of Escherichia coli ATP synthase.
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J Biol Chem,
280,
27981-27989.
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C.Kluge,
T.Seidel,
S.Bolte,
S.S.Sharma,
M.Hanitzsch,
B.Satiat-Jeunemaitre,
J.Ross,
M.Sauer,
D.Golldack,
and
K.J.Dietz
(2004).
Subcellular distribution of the V-ATPase complex in plant cells, and in vivo localisation of the 100 kDa subunit VHA-a within the complex.
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BMC Cell Biol,
5,
29.
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D.M.Mueller,
N.Puri,
V.Kabaleeswaran,
C.Terry,
A.G.Leslie,
and
J.E.Walker
(2004).
Crystallization and preliminary crystallographic studies of the mitochondrial F1-ATPase from the yeast Saccharomyces cerevisiae.
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Acta Crystallogr D Biol Crystallogr,
60,
1441-1444.
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M.Müller,
K.Gumbiowski,
D.A.Cherepanov,
S.Winkler,
W.Junge,
S.Engelbrecht,
and
O.Pänke
(2004).
Rotary F1-ATPase. Is the C-terminus of subunit gamma fixed or mobile?
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Eur J Biochem,
271,
3914-3922.
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R.Kagawa,
M.G.Montgomery,
K.Braig,
A.G.Leslie,
and
J.E.Walker
(2004).
The structure of bovine F1-ATPase inhibited by ADP and beryllium fluoride.
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EMBO J,
23,
2734-2744.
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PDB codes:
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Z.Ahmad,
and
A.E.Senior
(2004).
Mutagenesis of residue betaArg-246 in the phosphate-binding subdomain of catalytic sites of Escherichia coli F1-ATPase.
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J Biol Chem,
279,
31505-31513.
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Z.Ahmad,
and
A.E.Senior
(2004).
Role of betaAsn-243 in the phosphate-binding subdomain of catalytic sites of Escherichia coli F(1)-ATPase.
|
| |
J Biol Chem,
279,
46057-46064.
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E.Cabezón,
M.G.Montgomery,
A.G.Leslie,
and
J.E.Walker
(2003).
The structure of bovine F1-ATPase in complex with its regulatory protein IF1.
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Nat Struct Biol,
10,
744-750.
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PDB code:
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M.D.Greene,
and
W.D.Frasch
(2003).
Interactions among gamma R268, gamma Q269, and the beta subunit catch loop of Escherichia coli F1-ATPase are important for catalytic activity.
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J Biol Chem,
278,
51594-51598.
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M.Dittrich,
S.Hayashi,
and
K.Schulten
(2003).
On the mechanism of ATP hydrolysis in F1-ATPase.
|
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Biophys J,
85,
2253-2266.
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R.E.Marquis,
S.A.Clock,
and
M.Mota-Meira
(2003).
Fluoride and organic weak acids as modulators of microbial physiology.
|
| |
FEMS Microbiol Rev,
26,
493-510.
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W.Yang,
Y.Q.Gao,
Q.Cui,
J.Ma,
and
M.Karplus
(2003).
The missing link between thermodynamics and structure in F1-ATPase.
|
| |
Proc Natl Acad Sci U S A,
100,
874-879.
|
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A.Cook,
E.D.Lowe,
E.D.Chrysina,
V.T.Skamnaki,
N.G.Oikonomakos,
and
L.N.Johnson
(2002).
Structural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism.
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Biochemistry,
41,
7301-7311.
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PDB code:
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E.E.Fetsch,
and
A.L.Davidson
(2002).
Vanadate-catalyzed photocleavage of the signature motif of an ATP-binding cassette (ABC) transporter.
|
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Proc Natl Acad Sci U S A,
99,
9685-9690.
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Madhusudan,
P.Akamine,
N.H.Xuong,
and
S.S.Taylor
(2002).
Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase.
|
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Nat Struct Biol,
9,
273-277.
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PDB code:
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P.D.Boyer
(2001).
New insights into one of nature's remarkable catalysts, the ATP synthase.
|
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Mol Cell,
8,
246-247.
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R.I.Menz,
J.E.Walker,
and
A.G.Leslie
(2001).
Structure of bovine mitochondrial F(1)-ATPase with nucleotide bound to all three catalytic sites: implications for the mechanism of rotary catalysis.
|
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Cell,
106,
331-341.
|
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PDB codes:
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T.K.Sixma
(2001).
DNA mismatch repair: MutS structures bound to mismatches.
|
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Curr Opin Struct Biol,
11,
47-52.
|
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T.Murata,
Y.Kakinuma,
and
I.Yamato
(2001).
ATP-dependent affinity change of Na+-binding sites of V-ATPase.
|
| |
J Biol Chem,
276,
48337-48340.
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D.Stock,
C.Gibbons,
I.Arechaga,
A.G.Leslie,
and
J.E.Walker
(2000).
The rotary mechanism of ATP synthase.
|
| |
Curr Opin Struct Biol,
10,
672-679.
|
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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.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
