PDBsum entry 1e1r

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protein ligands metals Protein-protein interface(s) links
Atp phosphorylase PDB id
Jmol PyMol
Protein chains
487 a.a. *
467 a.a. *
122 a.a. *
ANP ×4
_MG ×5
Waters ×860
* Residue conservation analysis
PDB id:
Name: Atp phosphorylase
Title: Bovine mitochondrial f1-atpase inhibited by mg2+adp and aluminium fluoride
Structure: 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.
Source: Bos taurus. Bovine. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Organelle: mitochondrion. Organelle: mitochondrion
Biol. unit: Heptamer (from PQS)
2.50Å     R-factor:   0.218     R-free:   0.282
Authors: K.Braig,R.I.Menz,M.G.Montgomery,A.G.W.Leslie,J.E.Walker
Key ref:
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: 10873854 DOI: 10.1016/S0969-2126(00)00145-3
10-May-00     Release date:   28-Jun-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P19483  (ATPA_BOVIN) -  ATP synthase subunit alpha, mitochondrial
553 a.a.
487 a.a.*
Protein chains
Pfam   ArchSchema ?
P00829  (ATPB_BOVIN) -  ATP synthase subunit beta, mitochondrial
528 a.a.
467 a.a.
Protein chain
Pfam   ArchSchema ?
P05631  (ATPG_BOVIN) -  ATP synthase subunit gamma, mitochondrial
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.  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
+ H(2)O
+ H(+)(In)
Bound ligand (Het Group name = ADP)
corresponds exactly
Bound ligand (Het Group name = PO4)
corresponds exactly
+ H(+)(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   14 terms 
  Biological process     transport   13 terms 
  Biochemical function     nucleotide binding     11 terms  


DOI no: 10.1016/S0969-2126(00)00145-3 Structure 8:567-573 (2000)
PubMed id: 10873854  
Structure of bovine mitochondrial F(1)-ATPase inhibited by Mg(2+) ADP and aluminium fluoride.
K.Braig, R.I.Menz, M.G.Montgomery, A.G.Leslie, J.E.Walker.
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.
  Selected figure(s)  
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].
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 567-573) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21151115 I.G.Muñoz, H.Yébenes, M.Zhou, P.Mesa, M.Serna, A.Y.Park, E.Bragado-Nilsson, A.Beloso, 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.
  Nat Struct Mol Biol, 18, 14-19.
PDB code: 2xsm
21481781 K.Okazaki, and S.Takada (2011).
Structural Comparison of F(1)-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations.
  Structure, 19, 588-598.  
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.  
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
19240022 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.
  J Biol Chem, 284, 10747-10754.  
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.  
18628203 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.  
18339602 M.Nakanishi-Matsui, and M.Futai (2008).
Stochastic rotational catalysis of proton pumping F-ATPase.
  Philos Trans R Soc Lond B Biol Sci, 363, 2135-2142.  
18647240 N.D.Thomsen, and J.M.Berger (2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
  Mol Microbiol, 69, 1071-1090.  
18515057 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.  
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
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.  
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
17766379 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.
  Protein Sci, 16, 2118-2122.  
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.  
15642265 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.
  Structure, 13, 99.
PDB codes: 1xpo 1xpr 1xpu
16203732 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.
  J Biol Chem, 280, 40130-40134.  
15939739 Z.Ahmad, and A.E.Senior (2005).
Modulation of charge in the phosphate binding site of Escherichia coli ATP synthase.
  J Biol Chem, 280, 27981-27989.  
15310389 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.
  BMC Cell Biol, 5, 29.  
15272171 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.
  Acta Crystallogr D Biol Crystallogr, 60, 1441-1444.  
15373837 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?
  Eur J Biochem, 271, 3914-3922.  
15229653 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.
  EMBO J, 23, 2734-2744.
PDB codes: 1w0j 1w0k
15150266 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.
  J Biol Chem, 279, 31505-31513.  
15322126 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.  
12923572 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.
  Nat Struct Biol, 10, 744-750.
PDB code: 1ohh
14532272 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.
  J Biol Chem, 278, 51594-51598.  
14507690 M.Dittrich, S.Hayashi, and K.Schulten (2003).
On the mechanism of ATP hydrolysis in F1-ATPase.
  Biophys J, 85, 2253-2266.  
12586392 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.  
12552084 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.  
12044161 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.
  Biochemistry, 41, 7301-7311.
PDB code: 1gy3
12093921 E.E.Fetsch, and A.L.Davidson (2002).
Vanadate-catalyzed photocleavage of the signature motif of an ATP-binding cassette (ABC) transporter.
  Proc Natl Acad Sci U S A, 99, 9685-9690.  
11896404 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.
  Nat Struct Biol, 9, 273-277.
PDB code: 1l3r
11545726 P.D.Boyer (2001).
New insights into one of nature's remarkable catalysts, the ATP synthase.
  Mol Cell, 8, 246-247.  
11509182 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.
  Cell, 106, 331-341.
PDB code: 1h8e
11179891 T.K.Sixma (2001).
DNA mismatch repair: MutS structures bound to mismatches.
  Curr Opin Struct Biol, 11, 47-52.  
  11557766 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.  
11114504 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.  
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.