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PDBsum entry 1h8h
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1h8h

 

 

 

 

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Contents
Protein chains
487 a.a. *
467 a.a. *
122 a.a. *
Ligands
ATP ×4
GOL
ADP
PO4
Metals
_MG ×5
Waters ×111
* Residue conservation analysis
PDB id:
1h8h
Name: Hydrolase
Title: Bovine mitochondrial f1-atpase crystallised in the presence of 5mm amppnp
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. Cattle. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Organelle: mitochondrion. Organelle: mitochondrion
Biol. unit: Heptamer (from PQS)
Resolution:
2.90Å     R-factor:   0.236     R-free:   0.292
Authors: K.Braig,R.I.Menz,M.G.Montgomery,A.G.W.Leslie,J.E.Walker
Key ref:
R.I.Menz et al. (2001). The structure and nucleotide occupancy of bovine mitochondrial F(1)-ATPase are not influenced by crystallisation at high concentrations of nucleotide. FEBS Lett, 494, 11-14. PubMed id: 11297725 DOI: 10.1016/S0014-5793(01)02302-X
Date:
06-Feb-01     Release date:   15-Apr-01    
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
Bound ligand (Het Group name = ATP)
corresponds exactly 		+ H2O
 + 4 × H(+)(in)
 = ADP
 + 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: 10.1016/S0014-5793(01)02302-X FEBS Lett 494:11-14 (2001)
PubMed id: 11297725  
 
 
The structure and nucleotide occupancy of bovine mitochondrial F(1)-ATPase are not influenced by crystallisation at high concentrations of nucleotide.
R.I.Menz, A.G.Leslie, J.E.Walker.
 
  ABSTRACT  
 
Analysis of tryptophan mutants of F(1)-ATPase from Escherichia coli [Löbau et suggested that nucleotide concentrations used to grow crystals for the determination of the structure of bovine F(1)-ATPase would be sufficient to occupy only two catalytic sites, and that higher concentrations of nucleotide would result in all three sites being occupied. We have determined the structure of bovine F(1)-ATPase at 2.9 A resolution with crystals grown in the presence of 5 mM AMPPNP and 5 microM ADP. Similar to previous structures of bovine F(1)-ATPase determined with crystals grown in the presence of lower nucleotide concentrations, only two beta-subunits have bound nucleotide and the third subunit remains empty.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Stereo view of a superposition of the β[E] catalytic sites of the high AMPPNP and frozen-native [16] structures. All α-carbon atoms were used to superimpose the β[E]-subunits with rmsd of 0.15 Å. There is a slightly larger difference in the position of the bound phosphate (or sulphate) group, but this group has a very high temperature factor (80 Å^2). The carbon, nitrogen, oxygen and phosphorous atoms are coloured yellow, blue, red and pink, respectively. The 2F[o]–F[c] electron density map for the high AMPPNP structure is shown contoured at 1.3 σ.
 
  The above figure is reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2001, 494, 11-14) copyright 2001.  

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.  
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.  
20371322 R.Shimo-Kon, E.Muneyuki, H.Sakai, K.Adachi, M.Yoshida, and K.Kinosita (2010).
Chemo-mechanical coupling in F(1)-ATPase revealed by catalytic site occupancy during catalysis.
  Biophys J, 98, 1227-1236.  
20370611 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.  
19353640 E.Dodson, and G.Dodson (2009).
Movements at the hemoglobin A-hemes and their role in ligand binding, analyzed by X-ray crystallography.
  Biopolymers, 91, 1056-1063.  
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.  
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.  
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
17360523 V.V.Bulygin, and Y.M.Milgrom (2007).
Studies of nucleotide binding to the catalytic sites of Escherichia coli betaY331W-F1-ATPase using fluorescence quenching.
  Proc Natl Acad Sci U S A, 104, 4327-4331.  
17517661 Y.Togashi, and A.S.Mikhailov (2007).
Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines.
  Proc Natl Acad Sci U S A, 104, 8697-8702.  
15454080 D.Gai, R.Zhao, D.Li, C.V.Finkielstein, and X.S.Chen (2004).
Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen.
  Cell, 119, 47-60.
PDB codes: 1svl 1svm 1svo
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
14585932 W.Zheng, and S.Doniach (2003).
A comparative study of motor-protein motions by using a simple elastic-network model.
  Proc Natl Acad Sci U S A, 100, 13253-13258.  
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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