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PDBsum entry 1w0k
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1w0k

 

 

 

 

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Contents
Protein chains
487 a.a. *
467 a.a. *
122 a.a. *
Ligands
ADP ×5
GOL ×3
PO4
Metals
_MG ×5
Waters ×266
* Residue conservation analysis
PDB id:
1w0k
Name: Hydrolase
Title: Adp inhibited bovine f1-atpase
Structure: Atp synthase alpha chain heart isoform, mitochondrial precursor. Chain: a, b, c. Synonym: bovine mitochondrial f1-atpase\, alpha chain. Atp synthase beta chain, mitochondrial precursor. Chain: d, e, f. Synonym: bovine mitochondrial f1-atpase\, beta chain. Atp synthase gamma chain, mitochondrial precursor. Chain: g.
Source: Bos taurus. Bovine. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Tissue: muscle
Biol. unit: Heptamer (from PDB file)
Resolution:
2.85Å     R-factor:   0.225     R-free:   0.278
Authors: R.Kagawa,M.G.Montgomery,K.Braig,J.E.Walker,A.G.W.Leslie
Key ref:
R.Kagawa et al. (2004). The structure of bovine F1-ATPase inhibited by ADP and beryllium fluoride. EMBO J, 23, 2734-2744. PubMed id: 15229653 DOI: 10.1038/sj.emboj.7600293
Date:
08-Jun-04     Release date:   08-Jul-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19483  (ATPA_BOVIN) -  ATP synthase subunit alpha, mitochondrial from Bos taurus
Seq:
Struc: 		 
Seq:
Struc: 		553 a.a.
487 a.a.*
Protein chains
Pfam   ArchSchema ?
P00829  (ATPB_BOVIN) -  ATP synthase subunit beta, mitochondrial from Bos taurus
Seq:
Struc: 		 
Seq:
Struc: 		528 a.a.
467 a.a.
Protein chain
Pfam   ArchSchema ?
P05631  (ATPG_BOVIN) -  ATP synthase subunit gamma, mitochondrial from Bos taurus
Seq:
Struc: 		298 a.a.
122 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains D, E, F: E.C.7.1.2.2  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + 4 H+(in) = ADP + phosphate + 5 H+(out)
ATP
 + H2O
 + 4 × H(+)(in)
 =
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ phosphate
 + 5 × H(+)(out)
Bound ligand (Het Group name = PO4)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1038/sj.emboj.7600293 EMBO J 23:2734-2744 (2004)
PubMed id: 15229653  
 
 
The structure of bovine F1-ATPase inhibited by ADP and beryllium fluoride.
R.Kagawa, M.G.Montgomery, K.Braig, A.G.Leslie, J.E.Walker.
 
  ABSTRACT  
 
The structure of bovine F1-ATPase inhibited with ADP and beryllium fluoride at 2.0 angstroms resolution contains two ADP.BeF3- complexes mimicking ATP, bound in the catalytic sites of the beta(TP) and beta(DP) subunits. Except for a 1 angstrom shift in the guanidinium of alphaArg373, the conformations of catalytic side chains are very similar in both sites. However, the ordered water molecule that carries out nucleophilic attack on the gamma-phosphate of ATP during hydrolysis is 2.6 angstroms from the beryllium in the beta(DP) subunit and 3.8 angstroms away in the beta(TP) subunit, strongly indicating that the beta(DP) subunit is the catalytically active conformation. In the structure of F1-ATPase with five bound ADP molecules (three in alpha-subunits, one each in the beta(TP) and beta(DP) subunits), which has also been determined, the conformation of alphaArg373 suggests that it senses the presence (or absence) of the gamma-phosphate of ATP. Two catalytic schemes are discussed concerning the various structures of bovine F1-ATPase.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Superimposition of nucleotide-binding site residues in the [TP] subunits in the structures of bovine ADP-F[1] and BeF[3]^--F[1]. The view is shown in stereo and the ADP-F[1] and BeF[3]^--F[1] structures are coloured and grey, respectively. The [TP]Arg373 side chain adopts dramatically different conformations in the two structures as does [TP]Phe424. 		Figure 6.
Figure 6 Two possible reaction schemes for ATP hydrolysis by F[1]-ATPase. In parts (A) and (B) F[1]-ATPase is depicted as viewed from the membrane proximal aspect of the intact ATP synthase. For simplicity, only the catalytic -subunits and the centrally located -subunit are shown. ATP^* represents an ATP molecule that is committed to hydrolysis. See text for further details.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2734-2744) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23334411 S.Arai, S.Saijo, K.Suzuki, K.Mizutani, Y.Kakinuma, Y.Ishizuka-Katsura, N.Ohsawa, T.Terada, M.Shirouzu, S.Yokoyama, S.Iwata, I.Yamato, and T.Murata (2013).
Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures.
  Nature, 493, 703-707.
PDB codes: 3vr2 3vr3 3vr4 3vr5 3vr6
21481781 K.Okazaki, and S.Takada (2011).
Structural Comparison of F(1)-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations.
  Structure, 19, 588-598.  
21734658 P.Wollmann, S.Cui, R.Viswanathan, O.Berninghausen, M.N.Wells, M.Moldt, G.Witte, A.Butryn, P.Wendler, R.Beckmann, D.T.Auble, and K.P.Hopfner (2011).
Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP.
  Nature, 475, 403-407.
PDB codes: 3oc3 3oci
21113137 Y.Murayama, A.Mukaiyama, K.Imai, Y.Onoue, A.Tsunoda, A.Nohara, T.Ishida, Y.Maéda, K.Terauchi, T.Kondo, and S.Akiyama (2011).
Tracking and visualizing the circadian ticking of the cyanobacterial clock protein KaiC in solution.
  EMBO J, 30, 68-78.  
20300495 H.J.Bernstein, and P.A.Craig (2010).
Efficient molecular surface rendering by linear-time pseudo-Gaussian approximation to Lee-Richards surfaces (PGALRS).
  J Appl Crystallogr, 43, 356-361.  
20644710 P.Balabaskaran Nina, N.V.Dudkina, L.A.Kane, J.E.van Eyk, E.J.Boekema, M.W.Mather, and A.B.Vaidya (2010).
Highly divergent mitochondrial ATP synthase complexes in Tetrahymena thermophila.
  PLoS Biol, 8, e1000418.  
20871600 R.Watanabe, R.Iino, and H.Noji (2010).
Phosphate release in F1-ATPase catalytic cycle follows ADP release.
  Nat Chem Biol, 6, 814-820.  
20336770 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.  
20689227 Y.Kagawa (2010).
ATP synthase: from single molecule to human bioenergetics.
  Proc Jpn Acad Ser B Phys Biol Sci, 86, 667-693.  
19610671 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.  
19033377 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.
  RNA, 15, 67-75.
PDB code: 3ex7
19477165 L.S.Chen, B.J.Nowak, M.L.Ayres, N.L.Krett, S.T.Rosen, S.Zhang, and V.Gandhi (2009).
Inhibition of ATP synthase by chlorinated adenosine analogue.
  Biochem Pharmacol, 78, 583-591.  
19879839 N.D.Thomsen, and J.M.Berger (2009).
Running in reverse: the structural basis for translocation polarity in hexameric helicases.
  Cell, 139, 523-534.
PDB code: 3ice
19280602 W.Zheng (2009).
Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase.
  Proteins, 76, 747-762.  
18846414 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.  
19075235 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.  
18329872 E.J.Enemark, and L.Joshua-Tor (2008).
On helicases and other motor proteins.
  Curr Opin Struct Biol, 18, 243-257.  
19088201 F.Liu, A.Putnam, and E.Jankowsky (2008).
ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding.
  Proc Natl Acad Sci U S A, 105, 20209-20214.  
18723591 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.  
19052322 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.  
19011636 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.  
17697996 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: 2qe7
17255937 A.Yamagata, and J.A.Tainer (2007).
Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism.
  EMBO J, 26, 878-890.
PDB codes: 2oap 2oaq
17904517 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.
  Biochim Biophys Acta, 1767, 1319-1330.  
18003896 H.Z.Mao, and J.Weber (2007).
Identification of the betaTP site in the x-ray structure of F1-ATPase as the high-affinity catalytic site.
  Proc Natl Acad Sci U S A, 104, 18478-18483.  
17698806 J.R.Gledhill, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2007).
Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols.
  Proc Natl Acad Sci U S A, 104, 13632-13637.
PDB codes: 2jiz 2jj1 2jj2
17895376 J.R.Gledhill, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2007).
How the regulatory protein, IF(1), inhibits F(1)-ATPase from bovine mitochondria.
  Proc Natl Acad Sci U S A, 104, 15671-15676.
PDB code: 2v7q
17662945 K.Adachi, K.Oiwa, T.Nishizaka, S.Furuike, H.Noji, H.Itoh, M.Yoshida, and K.Kinosita (2007).
Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation.
  Cell, 130, 309-321.  
17350959 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.
  J Biol Chem, 282, 14238-14242.
PDB code: 2jdi
16828083 H.Z.Mao, W.D.Gray, and J.Weber (2006).
Does F1-ATPase have a catalytic site that preferentially binds MgADP?
  FEBS Lett, 580, 4131-4135.  
  16754973 J.A.Silvester, V.K.Dickson, M.J.Runswick, A.G.Leslie, and J.E.Walker (2006).
The expression, purification, crystallization and preliminary X-ray analysis of a subcomplex of the peripheral stalk of ATP synthase from bovine mitochondria.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 530-533.  
16730323 J.Weber (2006).
ATP synthase: subunit-subunit interactions in the stator stalk.
  Biochim Biophys Acta, 1757, 1162-1170.  
16929099 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.
  Acta Crystallogr D Biol Crystallogr, 62, 991-995.  
16728506 M.W.Bowler, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2006).
How azide inhibits ATP hydrolysis by the F-ATPases.
  Proc Natl Acad Sci U S A, 103, 8646-8649.
PDB codes: 2ck3 2lcd
16990434 N.J.Baxter, L.F.Olguin, M.Golicnik, G.Feng, A.M.Hounslow, W.Bermel, G.M.Blackburn, F.Hollfelder, J.P.Waltho, and N.H.Williams (2006).
A Trojan horse transition state analogue generated by MgF3- formation in an enzyme active site.
  Proc Natl Acad Sci U S A, 103, 14732-14737.  
17082766 V.Kabaleeswaran, N.Puri, J.E.Walker, A.G.Leslie, and D.M.Mueller (2006).
Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1 ATPase.
  EMBO J, 25, 5433-5442.
PDB code: 2hld
16844693 Z.E.Sauna, K.Nandigama, and S.V.Ambudkar (2006).
Exploiting reaction intermediates of the ATPase reaction to elucidate the mechanism of transport by P-glycoprotein (ABCB1).
  J Biol Chem, 281, 26501-26511.  
16339725 C.P.Smith, and P.E.Thorsness (2005).
Formation of an energized inner membrane in mitochondria with a gamma-deficient F1-ATPase.
  Eukaryot Cell, 4, 2078-2086.  
15665871 E.R.Goedken, S.L.Kazmirski, G.D.Bowman, M.O'Donnell, and J.Kuriyan (2005).
Mapping the interaction of DNA with the Escherichia coli DNA polymerase clamp loader complex.
  Nat Struct Mol Biol, 12, 183-190.  
16217018 J.Xing, J.C.Liao, and G.Oster (2005).
Making ATP.
  Proc Natl Acad Sci U S A, 102, 16539-16546.  
15870208 M.Karplus, and J.Kuriyan (2005).
Molecular dynamics and protein function.
  Proc Natl Acad Sci U S A, 102, 6679-6685.  
15758075 Y.Hirono-Hara, K.Ishizuka, K.Kinosita, M.Yoshida, and H.Noji (2005).
Activation of pausing F1 motor by external force.
  Proc Natl Acad Sci U S A, 102, 4288-4293.  
15540116 O.Drory, F.Frolow, and N.Nelson (2004).
Crystal structure of yeast V-ATPase subunit C reveals its stator function.
  EMBO Rep, 5, 1148-1152.
PDB code: 1u7l
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 codes are shown on the right.

 

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