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Contents |
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492 a.a.
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467 a.a.
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263 a.a.
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131 a.a.
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47 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Hydrolase
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Title:
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Bovine f1-atpase inhibited by dccd (dicyclohexylcarbodiimide)
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Structure:
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Atp synthase alpha chain heart isoform. Chain: a, b, c. Synonym: bovine mitochondrial f1-atpase. Atp synthase beta chain. Chain: d, e, f. Synonym: bovine mitochondrial f1-atpase. Atp synthase gamma chain. Chain: g. Synonym: bovine mitochondrial f1-atpase.
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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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Nonamer (from
)
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Resolution:
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2.40Å
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R-factor:
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0.225
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R-free:
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0.281
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Authors:
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C.Gibbons,M.G.Montgomery,A.G.W.Leslie,J.E.Walker
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Key ref:
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C.Gibbons
et al.
(2000).
The structure of the central stalk in bovine F(1)-ATPase at 2.4 A resolution.
Nat Struct Biol,
7,
1055-1061.
PubMed id:
DOI:
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Date:
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25-Aug-00
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Release date:
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03-Nov-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.
492 a.a.*
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P00829
(ATPB_BOVIN) -
ATP synthase subunit beta, mitochondrial from Bos taurus
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Seq:
Struc:
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528 a.a.
467 a.a.
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P05631
(ATPG_BOVIN) -
ATP synthase subunit gamma, mitochondrial from Bos taurus
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Seq:
Struc:
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298 a.a.
263 a.a.
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Enzyme class 2:
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Chains A, B, C, G, H, I:
E.C.3.6.1.34
- Transferred entry: 7.1.2.2.
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Enzyme class 3:
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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
Bound ligand (Het Group name = )
corresponds exactly
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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
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+
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phosphate
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+
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5
×
H(+)(out)
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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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Nat Struct Biol
7:1055-1061
(2000)
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PubMed id:
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| |
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The structure of the central stalk in bovine F(1)-ATPase at 2.4 A resolution.
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C.Gibbons,
M.G.Montgomery,
A.G.Leslie,
J.E.Walker.
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ABSTRACT
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The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in
the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic
mechanism. The gamma subunit penetrates the catalytic (alpha beta)(3) domain and
protrudes beneath it, interacting with a ring of c subunits in the membrane that
drives rotation of the stalk during ATP synthesis. In other crystals of
F(1)-ATPase, the protrusion was disordered, but with crystals of F(1)-ATPase
inhibited with dicyclohexylcarbodiimide, the complete structure was revealed.
The delta and epsilon subunits interact with a Rossmann fold in the gamma
subunit, forming a foot. In ATP synthase, this foot interacts with the c-ring
and couples the transmembrane proton motive force to catalysis in the (alpha
beta)(3) domain.
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Selected figure(s)
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Figure 2.
Figure 2. The structure of the central stalk. The color code
for subunits is the same as in Fig. 1. The light blue regions
have been described in earlier structures and new regions of
structure in the  subunit
are dark blue. a, Side-on stereo view of stalk subunits (same
view as in Fig. 1a). b, Stereo view of stalk subunits, rotated
90° with respect to ( a), viewed from the membrane.
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Figure 5.
Figure 5. Interaction of  gamma
Arg 75 with residues in the  and
 subunits
to form part of the catalytic 'catch'. Distances are in
Å.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2000,
7,
1055-1061)
copyright 2000.
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Figures were
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
|
|
|
|
|
|
G.Cingolani,
and
T.M.Duncan
(2011).
Structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli in an autoinhibited conformation.
|
| |
Nat Struct Mol Biol,
18,
701-707.
|
|
|
|
|
|
|
J.Czub,
and
H.Grubmüller
(2011).
Torsional elasticity and energetics of F1-ATPase.
|
| |
Proc Natl Acad Sci U S A,
108,
7408-7413.
|
|
|
|
|
|
|
J.E.Alard,
S.Hillion,
L.Guillevin,
A.Saraux,
J.O.Pers,
P.Youinou,
and
C.Jamin
(2011).
Autoantibodies to endothelial cell surface ATP synthase, the endogenous receptor for hsp60, might play a pathogenic role in vasculatides.
|
| |
PLoS One,
6,
e14654.
|
|
|
|
|
|
|
K.Okazaki,
and
S.Takada
(2011).
Structural Comparison of F(1)-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations.
|
| |
Structure,
19,
588-598.
|
|
|
|
|
|
|
O.Danış,
S.Demir,
A.Günel,
R.G.Aker,
M.Gülçebi,
F.Onat,
and
A.Ogan
(2011).
Changes in intracellular protein expression in cortex, thalamus and hippocampus in a genetic rat model of absence epilepsy.
|
| |
Brain Res Bull,
84,
381-388.
|
|
|
|
|
|
|
T.Beke-Somfai,
P.Lincoln,
and
B.Nordén
(2011).
Double-lock ratchet mechanism revealing the role of alphaSER-344 in FoF1 ATP synthase.
|
| |
Proc Natl Acad Sci U S A,
108,
4828-4833.
|
|
|
|
|
|
|
T.Ibuki,
K.Imada,
T.Minamino,
T.Kato,
T.Miyata,
and
K.Namba
(2011).
Common architecture of the flagellar type III protein export apparatus and F- and V-type ATPases.
|
| |
Nat Struct Mol Biol,
18,
277-282.
|
|
|
PDB code:
|
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|
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|
|
|
B.A.Feniouk,
Y.Kato-Yamada,
M.Yoshida,
and
T.Suzuki
(2010).
Conformational transitions of subunit epsilon in ATP synthase from thermophilic Bacillus PS3.
|
| |
Biophys J,
98,
434-442.
|
|
|
|
|
|
|
C.Hunke,
V.S.Tadwal,
M.S.Manimekalai,
M.Roessle,
and
G.Grüber
(2010).
The effect of NBD-Cl in nucleotide-binding of the major subunit alpha and B of the motor proteins F1FO ATP synthase and A1AO ATP synthase.
|
| |
J Bioenerg Biomembr,
42,
1.
|
|
|
|
|
|
|
D.Pogoryelov,
A.Krah,
J.D.Langer,
Ã.–.Yildiz,
J.D.Faraldo-Gómez,
and
T.Meier
(2010).
Microscopic rotary mechanism of ion translocation in the F(o) complex of ATP synthases.
|
| |
Nat Chem Biol,
6,
891-899.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.Yagi,
H.Konno,
T.Murakami-Fuse,
A.Isu,
T.Oroguchi,
H.Akutsu,
M.Ikeguchi,
and
T.Hisabori
(2010).
Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms.
|
| |
Biochem J,
425,
85-94.
|
|
|
PDB codes:
|
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|
|
|
|
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I.N.Watt,
M.G.Montgomery,
M.J.Runswick,
A.G.Leslie,
and
J.E.Walker
(2010).
Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria.
|
| |
Proc Natl Acad Sci U S A,
107,
16823-16827.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.A.Mayr,
V.Havlícková,
F.Zimmermann,
I.Magler,
V.Kaplanová,
P.Jesina,
A.Pecinová,
H.Nusková,
J.Koch,
W.Sperl,
and
J.Houstek
(2010).
Mitochondrial ATP synthase deficiency due to a mutation in the ATP5E gene for the F1 epsilon subunit.
|
| |
Hum Mol Genet,
19,
3430-3439.
|
|
|
|
|
|
|
V.V.Bulygin,
and
Y.M.Milgrom
(2010).
Probes of inhibition of Escherichia coli F(1)-ATPase by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole in the presence of MgADP and MgATP support a bi-site mechanism of ATP hydrolysis by the enzyme.
|
| |
Biochemistry (Mosc),
75,
327-335.
|
|
|
|
|
|
|
Y.Ito,
and
M.Ikeguchi
(2010).
Structural fluctuation and concerted motions in F(1)-ATPase: A molecular dynamics study.
|
| |
J Comput Chem,
31,
2175-2185.
|
|
|
|
|
|
|
Y.Kagawa
(2010).
ATP synthase: from single molecule to human bioenergetics.
|
| |
Proc Jpn Acad Ser B Phys Biol Sci,
86,
667-693.
|
|
|
|
|
|
|
Y.Pang,
H.Wang,
W.Q.Song,
and
Y.X.Zhu
(2010).
The cotton ATP synthase δ1 subunit is required to maintain a higher ATP/ADP ratio that facilitates rapid fibre cell elongation.
|
| |
Plant Biol (Stuttg),
12,
903-909.
|
|
|
|
|
|
|
Z.L.Hildenbrand,
S.K.Molugu,
D.Stock,
and
R.A.Bernal
(2010).
The C-H peripheral stalk base: a novel component in V1-ATPase assembly.
|
| |
PLoS One,
5,
e12588.
|
|
|
|
|
|
|
A.Y.Mulkidjanian,
M.Y.Galperin,
and
E.V.Koonin
(2009).
Co-evolution of primordial membranes and membrane proteins.
|
| |
Trends Biochem Sci,
34,
206-215.
|
|
|
|
|
|
|
D.Pogoryelov,
O.Yildiz,
J.D.Faraldo-Gómez,
and
T.Meier
(2009).
High-resolution structure of the rotor ring of a proton-dependent ATP synthase.
|
| |
Nat Struct Mol Biol,
16,
1068-1073.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.Spetzler,
R.Ishmukhametov,
T.Hornung,
L.J.Day,
J.Martin,
and
W.D.Frasch
(2009).
Single molecule measurements of F1-ATPase reveal an interdependence between the power stroke and the dwell duration.
|
| |
Biochemistry,
48,
7979-7985.
|
|
|
|
|
|
|
L.Bae,
and
S.B.Vik
(2009).
A more robust version of the Arginine 210-switched mutant in subunit a of the Escherichia coli ATP synthase.
|
| |
Biochim Biophys Acta,
1787,
1129-1134.
|
|
|
|
|
|
|
M.Rak,
X.Zeng,
J.J.Brière,
and
A.Tzagoloff
(2009).
Assembly of F0 in Saccharomyces cerevisiae.
|
| |
Biochim Biophys Acta,
1793,
108-116.
|
|
|
|
|
|
|
N.Mnatsakanyan,
A.M.Krishnakumar,
T.Suzuki,
and
J.Weber
(2009).
The Role of the {beta}DELSEED-loop of ATP Synthase.
|
| |
J Biol Chem,
284,
11336-11345.
|
|
|
|
|
|
|
N.Mnatsakanyan,
J.A.Hook,
L.Quisenberry,
and
J.Weber
(2009).
ATP synthase with its gamma subunit reduced to the N-terminal helix can still catalyze ATP synthesis.
|
| |
J Biol Chem,
284,
26519-26525.
|
|
|
|
|
|
|
N.Numoto,
Y.Hasegawa,
K.Takeda,
and
K.Miki
(2009).
Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase.
|
| |
EMBO Rep,
10,
1228-1234.
|
|
|
PDB codes:
|
|
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|
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|
|
R.Iino,
R.Hasegawa,
K.V.Tabata,
and
H.Noji
(2009).
Mechanism of inhibition by C-terminal alpha-helices of the epsilon subunit of Escherichia coli FoF1-ATP synthase.
|
| |
J Biol Chem,
284,
17457-17464.
|
|
|
|
|
|
|
W.Zheng
(2009).
Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase.
|
| |
Proteins,
76,
747-762.
|
|
|
|
|
|
|
A.F.Lodeyro,
M.V.Castelli,
and
O.A.Roveri
(2008).
ATP hydrolysis-driven H(+) translocation is stimulated by sulfate, a strong inhibitor of mitochondrial ATP synthesis.
|
| |
J Bioenerg Biomembr,
40,
269-279.
|
|
|
|
|
|
|
A.Y.Mulkidjanian,
M.Y.Galperin,
K.S.Makarova,
Y.I.Wolf,
and
E.V.Koonin
(2008).
Evolutionary primacy of sodium bioenergetics.
|
| |
Biol Direct,
3,
13.
|
|
|
|
|
|
|
D.J.Cipriano,
and
S.D.Dunn
(2008).
Tethering polypeptides through bifunctional PEG cross-linking agents to probe protein function: application to ATP synthase.
|
| |
Proteins,
73,
458-467.
|
|
|
|
|
|
|
D.Okuno,
R.Fujisawa,
R.Iino,
Y.Hirono-Hara,
H.Imamura,
and
H.Noji
(2008).
Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation.
|
| |
Proc Natl Acad Sci U S A,
105,
20722-20727.
|
|
|
|
|
|
|
D.Pogoryelov,
Y.Nikolaev,
U.Schlattner,
K.Pervushin,
P.Dimroth,
and
T.Meier
(2008).
Probing the rotor subunit interface of the ATP synthase from Ilyobacter tartaricus.
|
| |
FEBS J,
275,
4850-4862.
|
|
|
|
|
|
|
G.I.Belogrudov
(2008).
The proximal N-terminal amino acid residues are required for the coupling activity of the bovine heart mitochondrial factor B.
|
| |
Arch Biochem Biophys,
473,
76-87.
|
|
|
|
|
|
|
H.Shen,
D.E.Walters,
and
D.M.Mueller
(2008).
Introduction of the chloroplast redox regulatory region in the yeast ATP synthase impairs cytochrome C oxidase.
|
| |
J Biol Chem,
283,
32937-32943.
|
|
|
|
|
|
|
H.Sielaff,
H.Rennekamp,
S.Engelbrecht,
and
W.Junge
(2008).
Functional halt positions of rotary FOF1-ATPase correlated with crystal structures.
|
| |
Biophys J,
95,
4979-4987.
|
|
|
|
|
|
|
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.
|
| |
J Biol Chem,
283,
26228-26240.
|
|
|
|
|
|
|
J.J.García-Trejo,
and
E.Morales-Ríos
(2008).
Regulation of the F(1)F (0)-ATP Synthase Rotary Nanomotor in its Monomeric-Bacterial and Dimeric-Mitochondrial Forms.
|
| |
J Biol Phys,
34,
197-212.
|
|
|
|
|
|
|
J.Pu,
and
M.Karplus
(2008).
How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase.
|
| |
Proc Natl Acad Sci U S A,
105,
1192-1197.
|
|
|
|
|
|
|
M.D.Hossain,
S.Furuike,
Y.Maki,
K.Adachi,
T.Suzuki,
A.Kohori,
H.Itoh,
M.Yoshida,
and
K.Kinosita
(2008).
Neither helix in the coiled coil region of the axle of F1-ATPase plays a significant role in torque production.
|
| |
Biophys J,
95,
4837-4844.
|
|
|
|
|
|
|
M.Hüttemann,
I.Lee,
A.Pecinova,
P.Pecina,
K.Przyklenk,
and
J.W.Doan
(2008).
Regulation of oxidative phosphorylation, the mitochondrial membrane potential, and their role in human disease.
|
| |
J Bioenerg Biomembr,
40,
445-456.
|
|
|
|
|
|
|
R.K.Nakamoto,
J.A.Baylis Scanlon,
and
M.K.Al-Shawi
(2008).
The rotary mechanism of the ATP synthase.
|
| |
Arch Biochem Biophys,
476,
43-50.
|
|
|
|
|
|
|
S.Furuike,
M.D.Hossain,
Y.Maki,
K.Adachi,
T.Suzuki,
A.Kohori,
H.Itoh,
M.Yoshida,
and
K.Kinosita
(2008).
Axle-less F1-ATPase rotates in the correct direction.
|
| |
Science,
319,
955-958.
|
|
|
|
|
|
|
S.Gayen,
A.M.Balakrishna,
G.Biuković,
W.Yulei,
C.Hunke,
and
G.Grüber
(2008).
Identification of critical residues of subunit H in its interaction with subunit E of the A-ATP synthase from Methanocaldococcus jannaschii.
|
| |
FEBS J,
275,
1803-1812.
|
|
|
|
|
|
|
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.
|
| |
Microbiol Mol Biol Rev,
72,
590.
|
|
|
|
|
|
|
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.
|
| |
Nat Struct Mol Biol,
15,
1326-1333.
|
|
|
|
|
|
|
A.Stocker,
S.Keis,
J.Vonck,
G.M.Cook,
and
P.Dimroth
(2007).
The structural basis for unidirectional rotation of thermoalkaliphilic F1-ATPase.
|
| |
Structure,
15,
904-914.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Y.Mulkidjanian,
K.S.Makarova,
M.Y.Galperin,
and
E.V.Koonin
(2007).
Inventing the dynamo machine: the evolution of the F-type and V-type ATPases.
|
| |
Nat Rev Microbiol,
5,
892-899.
|
|
|
|
|
|
|
B.A.Feniouk,
A.Rebecchi,
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Chromatophore vesicles of Rhodobacter capsulatus contain on average one F(O)F(1)-ATP synthase each.
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Biophys J,
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PDB code:
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PDB code:
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Proc Natl Acad Sci U S A,
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PDB codes:
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Large conformational changes of the epsilon subunit in the bacterial F1F0 ATP synthase provide a ratchet action to regulate this rotary motor enzyme.
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Proc Natl Acad Sci U S A,
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The rotary mechanism of ATP synthase.
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Where a reference describes a PDB structure, the PDB
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| |
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