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PDBsum entry 1cow

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protein ligands metals Protein-protein interface(s) links
Hydrogen ion transport PDB id
1cow
Jmol
Contents
Protein chains
487 a.a. *
467 a.a. *
122 a.a. *
Ligands
ANP ×4
ADP
AUR ×2
Metals
_MG ×5
Waters ×518
* Residue conservation analysis
PDB id:
1cow
Name: Hydrogen ion transport
Title: Bovine mitochondrial f1-atpase complexed with aurovertin b
Structure: Bovine mitochondrial f1-atpase. Chain: a, b, c. Bovine mitochondrial f1-atpase. Chain: d, e, f. Bovine mitochondrial f1-atpase. Chain: g. Ec: 3.6.1.34
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Organelle: mitochondrion. Organelle: mitochondrion
Biol. unit: Heptamer (from PQS)
Resolution:
3.10Å     R-factor:   0.231     R-free:   0.280
Authors: M.Van Raaij,J.P.Abrahams,A.G.W.Leslie,J.E.Walker
Key ref: M.J.van Raaij et al. (1996). The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B. Proc Natl Acad Sci U S A, 93, 6913-6917. PubMed id: 8692918
Date:
08-May-96     Release date:   17-Aug-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19483  (ATPA_BOVIN) -  ATP synthase subunit alpha, mitochondrial
Seq:
Struc:
 
Seq:
Struc:
553 a.a.
487 a.a.*
Protein chains
Pfam   ArchSchema ?
P00829  (ATPB_BOVIN) -  ATP synthase subunit beta, mitochondrial
Seq:
Struc:
 
Seq:
Struc:
528 a.a.
467 a.a.
Protein chain
Pfam   ArchSchema ?
P05631  (ATPG_BOVIN) -  ATP synthase subunit gamma, mitochondrial
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.3.6.3.14  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
ATP
+ H(2)O
+ H(+)(In)
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphate
+ H(+)(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   12 terms 
  Biological process     transport   12 terms 
  Biochemical function     nucleotide binding     10 terms  

 

 
    reference    
 
 
Proc Natl Acad Sci U S A 93:6913-6917 (1996)
PubMed id: 8692918  
 
 
The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B.
M.J.van Raaij, J.P.Abrahams, A.G.Leslie, J.E.Walker.
 
  ABSTRACT  
 
In the structure of bovine mitochondrial F1-ATPase that was previously determined with crystals grown in the presence of adenylyl-imidodiphosphate (AMP-PNP) and ADP, the three catalytic beta-subunits have different conformations and nucleotide occupancies. Adenylyl-imidodiphosphate is bound to one beta-subunit (betaTP), ADP is bound to the second (betaDP), and no nucleotide is bound to the third (betaE). Here we show that the uncompetitive inhibitor aurovertin B binds to bovine F1 at two equivalent sites in betaTP and betaE, in a cleft between the nucleotide binding and C-terminal domains. In betaDP, the aurovertin B pocket is incomplete and is inaccessible to the inhibitor. The aurovertin B bound to betaTP interacts with alpha-Glu399 in the adjacent alphaTP subunit, whereas the aurovertin B bound to betaE is too distant from alphaE to make an equivalent interaction. Both sites encompass betaArg-412, which was shown by mutational studies to be involved in binding aurovertin. Except for minor changes around the aurovertin pockets, the structure of bovine F1-ATPase is the same as determined previously. Aurovertin B appears to act by preventing closure of the catalytic interfaces, which is essential for a catalytic mechanism involving cyclic interconversion of catalytic sites.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21481781 K.Okazaki, and S.Takada (2011).
Structural Comparison of F(1)-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations.
  Structure, 19, 588-598.  
19768783 A.C.Stelzer, R.W.Frazee, C.Van Huis, J.Cleary, A.W.Opipari, G.D.Glick, and H.M.Al-Hashimi (2010).
NMR studies of an immunomodulatory benzodiazepine binding to its molecular target on the mitochondrial F(1)F(0)-ATPase.
  Biopolymers, 93, 85-92.  
20180002 V.Giorgio, E.Bisetto, R.Franca, D.A.Harris, S.Passamonti, and G.Lippe (2010).
The ectopic F(O)F(1) ATP synthase of rat liver is modulated in acute cholestasis by the inhibitor protein IF1.
  J Bioenerg Biomembr, 42, 117-123.  
20694228 Z.Y.Zhou, and J.K.Liu (2010).
Pigments of fungi (macromycetes).
  Nat Prod Rep, 27, 1531-1570.  
19462418 K.M.Johnson, L.Swenson, A.W.Opipari, R.Reuter, N.Zarrabi, C.A.Fierke, M.Börsch, and G.D.Glick (2009).
Mechanistic basis for differential inhibition of the F(1)F(o)-ATPase by aurovertin.
  Biopolymers, 91, 830-840.  
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.  
19644443 M.G.Düser, N.Zarrabi, D.J.Cipriano, S.Ernst, G.D.Glick, S.D.Dunn, and M.Börsch (2009).
36 degrees step size of proton-driven c-ring rotation in FoF1-ATP synthase.
  EMBO J, 28, 2689-2696.  
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.  
18579516 H.Z.Mao, C.G.Abraham, A.M.Krishnakumar, and J.Weber (2008).
A functionally important hydrogen-bonding network at the betaDP/alphaDP interface of ATP synthase.
  J Biol Chem, 283, 24781-24788.  
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.  
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
  17893896 T.Luo, and S.L.Schreiber (2007).
Complex alpha-pyrones synthesized by a gold-catalyzed coupling reaction.
  Angew Chem Int Ed Engl, 46, 8250-8253.  
16680033 E.Champagne, L.O.Martinez, X.Collet, and R.Barbaras (2006).
Ecto-F1Fo ATP synthase/F1 ATPase: metabolic and immunological functions.
  Curr Opin Lipidol, 17, 279-284.  
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
16156519 F.Wang, D.Q.Luo, and J.K.Liu (2005).
Aurovertin E, a new polyene pyrone from the basidiomycete Albatrellus confluens.
  J Antibiot (Tokyo), 58, 412-415.  
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
12944266 R.A.Böckmann, and H.Grubmüller (2003).
Conformational dynamics of the F1-ATPase beta-subunit: a molecular dynamics study.
  Biophys J, 85, 1482-1491.  
12360520 C.Minoletti, J.Santolini, F.Haraux, J.Pothier, and F.André (2002).
Rebuilt 3D structure of the chloroplast f1 ATPase-tentoxin complex.
  Proteins, 49, 302-320.  
11904410 G.Groth (2002).
Structure of spinach chloroplast F1-ATPase complexed with the phytopathogenic inhibitor tentoxin.
  Proc Natl Acad Sci U S A, 99, 3464-3468.
PDB code: 1kmh
11340051 B.E.Schultz, and S.I.Chan (2001).
Structures and proton-pumping strategies of mitochondrial respiratory enzymes.
  Annu Rev Biophys Biomol Struct, 30, 23-65.  
10836500 A.G.Leslie, and J.E.Walker (2000).
Structural model of F1-ATPase and the implications for rotary catalysis.
  Philos Trans R Soc Lond B Biol Sci, 355, 465-471.  
10882397 J.Zheng, and V.D.Ramirez (2000).
Inhibition of mitochondrial proton F0F1-ATPase/ATP synthase by polyphenolic phytochemicals.
  Br J Pharmacol, 130, 1115-1123.  
10632724 S.Günther, and B.Huchzermeyer (2000).
Nucleotide binding of an ADP analog to cooperating sites of chloroplast F1-ATPase (CF1).
  Eur J Biochem, 267, 541-548.  
  10477309 G.Schäfer, M.Engelhard, and V.Müller (1999).
Bioenergetics of the Archaea.
  Microbiol Mol Biol Rev, 63, 570-620.  
  10736751 N.B.Grodsky, and W.S.Allison (1999).
The adenine pocket of a single catalytic site is derivatized when the bovine heart mitochondrial F1-ATPase is photoinactivated with 4-amino-1-octylquinaldinium.
  Cell Biochem Biophys, 31, 285-294.  
9724515 J.Weber, S.Wilke-Mounts, S.T.Hammond, and A.E.Senior (1998).
Tryptophan substitutions surrounding the nucleotide in catalytic sites of F1-ATPase.
  Biochemistry, 37, 12042-12050.  
9784589 M.Hippler, K.Redding, and J.D.Rochaix (1998).
Chlamydomonas genetics, a tool for the study of bioenergetic pathways.
  Biochim Biophys Acta, 1367, 1.  
9692975 S.Löbau, J.Weber, and A.E.Senior (1998).
Catalytic site nucleotide binding and hydrolysis in F1F0-ATP synthase.
  Biochemistry, 37, 10846-10853.  
9242922 P.D.Boyer (1997).
The ATP synthase--a splendid molecular machine.
  Annu Rev Biochem, 66, 717-749.  
8790345 J.P.Abrahams, S.K.Buchanan, M.J.Van Raaij, I.M.Fearnley, A.G.Leslie, and J.E.Walker (1996).
The structure of bovine F1-ATPase complexed with the peptide antibiotic efrapeptin.
  Proc Natl Acad Sci U S A, 93, 9420-9424.
PDB code: 1efr
8961923 M.J.van Raaij, G.L.Orriss, M.G.Montgomery, M.J.Runswick, I.M.Fearnley, J.M.Skehel, and J.E.Walker (1996).
The ATPase inhibitor protein from bovine heart mitochondria: the minimal inhibitory sequence.
  Biochemistry, 35, 15618-15625.  
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.