spacer
spacer

PDBsum entry 1ohh

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Synthase PDB id
1ohh
Jmol
Contents
Protein chains
487 a.a. *
469 a.a. *
94 a.a. *
37 a.a. *
Ligands
ANP ×5
Metals
_MG ×5
* Residue conservation analysis
PDB id:
1ohh
Name: Synthase
Title: Bovine mitochondrial f1-atpase complexed with the inhibitor protein if1
Structure: Atp synthase alpha chain heart isoform, mitochondrial. Chain: a, b, c. Synonym: bovine mitochondrial f1-atpase alpha subunit. Atp synthase beta chain, mitochondrial. Chain: d, e, f. Synonym: bovine mitochondrial f1-atpase beta subunit. Atp synthase gamma chain, mitochondrial. Chain: g.
Source: Bos taurus. Bovine. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
Resolution:
2.80Å     R-factor:   0.232     R-free:   0.280
Ensemble: 2 models
Authors: E.Cabezon,M.G.Montgomery,A.G.W.Leslie,J.E.Walker
Key ref:
E.Cabezón et al. (2003). The structure of bovine F1-ATPase in complex with its regulatory protein IF1. Nat Struct Biol, 10, 744-750. PubMed id: 12923572 DOI: 10.1038/nsb966
Date:
27-May-03     Release date:   09-Jun-03    
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.
469 a.a.
Protein chain
Pfam   ArchSchema ?
P05631  (ATPG_BOVIN) -  ATP synthase subunit gamma, mitochondrial
Seq:
Struc:
298 a.a.
94 a.a.*
Protein chain
Pfam   ArchSchema ?
P01096  (ATIF1_BOVIN) -  ATPase inhibitor, mitochondrial
Seq:
Struc:
109 a.a.
37 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 38 residue positions (black crosses)

 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 = ANP)
matches with 81.00% similarity
+ 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   14 terms 
  Biochemical function     nucleotide binding     11 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nsb966 Nat Struct Biol 10:744-750 (2003)
PubMed id: 12923572  
 
 
The structure of bovine F1-ATPase in complex with its regulatory protein IF1.
E.Cabezón, M.G.Montgomery, A.G.Leslie, J.E.Walker.
 
  ABSTRACT  
 
In mitochondria, the hydrolytic activity of ATP synthase is prevented by an inhibitor protein, IF1. The active bovine protein (84 amino acids) is an alpha-helical dimer with monomers associated via an antiparallel alpha-helical coiled coil composed of residues 49-81. The N-terminal inhibitory sequences in the active dimer bind to two F1-ATPases in the presence of ATP. In the crystal structure of the F1-IF1 complex at 2.8 A resolution, residues 1-37 of IF1 bind in the alpha(DP)-beta(DP) interface of F1-ATPase, and also contact the central gamma subunit. The inhibitor opens the catalytic interface between the alpha(DP) and beta(DP) subunits relative to previous structures. The presence of ATP in the catalytic site of the beta(DP) subunit implies that the inhibited state represents a pre-hydrolysis step on the catalytic pathway of the enzyme.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo view of the contacts between F[1]-ATPase and IF[1]. Side chains from residues involved in contacts between F[1]-ATPase and IF[1] have been drawn. For details of the color scheme see the legend to Figure 1.
Figure 6.
Figure 6. The inhibition of the ATP hydrolytic activity of ATP synthase by IF[1]. The scheme is based on the binding change mechanism of ATP hydrolysis26. See text for further details.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 744-750) copyright 2003.  
  Figures were selected by an automated process.  

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.  
20235874 A.Caimari, P.Oliver, J.Keijer, and A.Palou (2010).
Peripheral blood mononuclear cells as a model to study the response of energy homeostasis-related genes to acute changes in feeding conditions.
  OMICS, 14, 129-141.  
20655344 D.W.Urry, K.D.Urry, W.Szaflarski, and M.Nowicki (2010).
Elastic-contractile model proteins: Physical chemistry, protein function and drug design and delivery.
  Adv Drug Deliv Rev, 62, 1404-1455.  
20689227 Y.Kagawa (2010).
ATP synthase: from single molecule to human bioenergetics.
  Proc Jpn Acad Ser B Phys Biol Sci, 86, 667-693.  
19299516 H.Diab, M.Ohira, M.Liu, E.Cobb, and P.M.Kane (2009).
Subunit Interactions and Requirements for Inhibition of the Yeast V1-ATPase.
  J Biol Chem, 284, 13316-13325.  
19096392 L.Shen, L.Zhi, W.Hu, and M.X.Wu (2009).
IEX-1 targets mitochondrial F1Fo-ATPase inhibitor for degradation.
  Cell Death Differ, 16, 603-612.  
19559621 M.Campanella, N.Parker, C.H.Tan, A.M.Hall, and M.R.Duchen (2009).
IF(1): setting the pace of the F(1)F(o)-ATP synthase.
  Trends Biochem Sci, 34, 343-350.  
17726461 C.Schmidt, E.Lepsverdize, S.L.Chi, A.M.Das, S.V.Pizzo, A.Dityatev, and M.Schachner (2008).
Amyloid precursor protein and amyloid beta-peptide bind to ATP synthase and regulate its activity at the surface of neural cells.
  Mol Psychiatry, 13, 953-969.  
18573072 C.von Ballmoos, G.M.Cook, and P.Dimroth (2008).
Unique rotary ATP synthase and its biological diversity.
  Annu Rev Biophys, 37, 43-64.  
18819926 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.  
18579516 H.Z.Mao, C.G.Abraham, A.M.Krishnakumar, and J.Weber (2008).
A Functionally Important Hydrogen-bonding Network at the {beta}DP/{alpha}DP Interface of ATP Synthase.
  J Biol Chem, 283, 24781-24788.  
  19669503 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.  
18156183 K.C.Jefferies, and M.Forgac (2008).
Subunit H of the vacuolar (H+) ATPase inhibits ATP hydrolysis by the free V1 domain by interaction with the rotary subunit F.
  J Biol Chem, 283, 4512-4519.  
18590689 M.Campanella, E.Casswell, S.Chong, Z.Farah, M.R.Wieckowski, A.Y.Abramov, A.Tinker, and M.R.Duchen (2008).
Regulation of mitochondrial structure and function by the F1Fo-ATPase inhibitor protein, IF1.
  Cell Metab, 8, 13-25.  
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.  
18326647 T.Hornung, O.A.Volkov, T.M.Zaida, S.Delannoy, J.G.Wise, and P.D.Vogel (2008).
Structure of the cytosolic part of the subunit b-dimer of Escherichia coli F0F1-ATP synthase.
  Biophys J, 94, 5053-5064.  
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
17492370 B.R.Francis, K.H.White, and P.E.Thorsness (2007).
Mutations in the Atp1p and Atp3p subunits of yeast ATP synthase differentially affect respiration and fermentation in Saccharomyces cerevisiae.
  J Bioenerg Biomembr, 39, 127-144.  
17286560 G.D.Clark-Walker (2007).
The F1-ATPase inhibitor Inh1 (IF1) affects suppression of mtDNA loss-lethality in Kluyveromyces lactis.
  FEMS Yeast Res, 7, 665-674.  
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
17851741 S.Contessi, M.Comelli, S.Cmet, G.Lippe, and I.Mavelli (2007).
IF(1) distribution in HepG2 cells in relation to ecto-F(0)F (1)ATPsynthase and calmodulin.
  J Bioenerg Biomembr, 39, 291-300.  
17517763 Y.C.Chen, Y.S.Lo, W.C.Hsu, and J.M.Yang (2007).
3D-partner: a web server to infer interacting partners and binding models.
  Nucleic Acids Res, 35, W561-W567.  
17244612 Y.Wang, U.Singh, and D.M.Mueller (2007).
Mitochondrial genome integrity mutations uncouple the yeast Saccharomyces cerevisiae ATP synthase.
  J Biol Chem, 282, 8228-8236.  
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.  
17049939 G.I.Belogrudov, V.Schirf, and B.Demeler (2006).
Reversible self-association of recombinant bovine factor B.
  Biochim Biophys Acta, 1764, 1741-1749.  
17019684 L.Domínguez-Ramírez, A.Gómez-Puyou, and M.T.de Gómez-Puyou (2006).
A hinge of the endogeneous ATP synthase inhibitor protein: the link between inhibitory and anchoring domains.
  Proteins, 65, 999.  
16365880 R.Carrozzo, I.Wittig, F.M.Santorelli, E.Bertini, S.Hofmann, U.Brandt, and H.Schägger (2006).
Subcomplexes of human ATP synthase mark mitochondrial biosynthesis disorders.
  Ann Neurol, 59, 265-275.  
16105947 F.Minauro-Sanmiguel, S.Wilkens, and J.J.García (2005).
Structure of dimeric mitochondrial ATP synthase: novel F0 bridging features and the structural basis of mitochondrial cristae biogenesis.
  Proc Natl Acad Sci U S A, 102, 12356-12358.  
15893664 J.Wang (2005).
Recent cyanobacterial Kai protein structures suggest a rotary clock.
  Structure, 13, 735-741.  
15640141 V.Corvest, C.Sigalat, R.Venard, P.Falson, D.M.Mueller, and F.Haraux (2005).
The binding mechanism of the yeast F1-ATPase inhibitory peptide: role of catalytic intermediates and enzyme turnover.
  J Biol Chem, 280, 9927-9936.  
14976187 B.Faustin, R.Rossignol, C.Rocher, G.Bénard, M.Malgat, and T.Letellier (2004).
Mobilization of adenine nucleotide translocators as molecular bases of the biochemical threshold effect observed in mitochondrial diseases.
  J Biol Chem, 279, 20411-20421.  
15692729 L.Domínguez-Ramírez, G.Garza-Ramos, H.Najera, G.Mendoza-Hernández, A.Gómez-Puyou, and M.T.de Gómez-Puyou (2004).
Interconversion between dimers and monomers of endogenous mitochondrial F1-inhibitor protein complexes and the release of the inhibitor protein. Spectroscopic characteristics of the complexes.
  J Bioenerg Biomembr, 36, 503-513.  
15128305 M.Galkin, R.Venard, J.Vaillier, J.Velours, and F.Haraux (2004).
Functional transitions of F0F1-ATPase mediated by the inhibitory peptide IF1 in yeast coupled submitochondrial particles.
  Eur J Biochem, 271, 1963-1970.  
15302203 M.R.Duchen (2004).
Mitochondria in health and disease: perspectives on a new mitochondrial biology.
  Mol Aspects Med, 25, 365-451.  
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
14633978 J.L.Rubinstein, J.E.Walker, and R.Henderson (2003).
Structure of the mitochondrial ATP synthase by electron cryomicroscopy.
  EMBO J, 22, 6182-6192.  
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.