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PDBsum entry 1nbm

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protein ligands metals Protein-protein interface(s) links
Atp synthase PDB id
1nbm
Jmol
Contents
Protein chains
487 a.a. *
467 a.a. *
122 a.a. *
Ligands
ATP ×4
ADP
PO4
Metals
_MG ×5
Waters ×164
* Residue conservation analysis
PDB id:
1nbm
Name: Atp synthase
Title: The structure of bovine f1-atpase covalently inhibited with 4-chloro-7-nitrobenzofurazan
Structure: F1-atpase. Chain: a, b, c. Synonym: bovine mithochondrial f1-atpase. F1-atpase. Chain: d, f. Synonym: bovine mithochondrial f1-atpase. F1-atpase. Chain: e. Synonym: bovine mithochondrial f1-atpase.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Organelle: mitochondrion. Organelle: mitochondrion
Biol. unit: Heptamer (from PQS)
Resolution:
3.00Å     R-factor:   0.207     R-free:   0.297
Authors: G.L.Orriss,A.G.W.Leslie,K.Braig,J.E.Walker
Key ref:
G.L.Orriss et al. (1998). Bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan: the structure provides further support for a rotary catalytic mechanism. Structure, 6, 831-837. PubMed id: 9687365 DOI: 10.1016/S0969-2126(98)00085-9
Date:
30-Apr-98     Release date:   26-Aug-98    
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
Bound ligand (Het Group name = ATP)
corresponds exactly
+ H(2)O
+ H(+)(In)
= ADP
+
phosphate
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   12 terms 
  Biological process     transport   13 terms 
  Biochemical function     nucleotide binding     10 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(98)00085-9 Structure 6:831-837 (1998)
PubMed id: 9687365  
 
 
Bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan: the structure provides further support for a rotary catalytic mechanism.
G.L.Orriss, A.G.Leslie, K.Braig, J.E.Walker.
 
  ABSTRACT  
 
BACKGROUND: F1-ATPase is the globular domain of F1F0-ATP synthase that catalyses the hydrolysis of ATP to ADP and phosphate. The crystal structure of bovine F1-ATPase has been determined previously to 2.8 A resolution. The enzyme comprises five different subunits in the stoichiometry alpha 3 beta 3 gamma delta epsilon; the three catalytic beta subunits alternate with the three alpha subunits around the centrally located single gamma subunit. To understand more about the catalytic mechanisms, F1-ATPase was inhibited by reaction with 4-chloro-7-nitrobenzofurazan (NBD-Cl) and the structure of the inhibited complex (F1-NBD) determined by X-ray crystallography. RESULTS: In the structure the three beta subunits adopt a different conformation with different nucleotide occupancy. NBD-Cl reacts with the phenolic oxygen of Tyr311 of the beta E subunit, which contains no bound nucleotide. The two other catalytic subunits beta TP and beta DP contain bound adenylyl-imidodiphosphate (AMP-PNP) and ADP, respectively. The binding site of the NBD moiety does not overlap with the regions of beta E that form the nucleotide-binding pocket in subunits beta TP and beta DP nor does it occlude the nucleotide-binding site. Catalysis appears to be inhibited because neither beta TP nor beta DP can accommodate a Tyr311 residue bearing an NBD group. CONCLUSIONS: The results presented here are consistent with a rotary catalytic mechanism of ATP synthesis and hydrolysis, which requires the sequential and concerted participation of all three catalytic sites. NBD-Cl inhibits the enzyme by preventing the modified subunit from adopting a conformation that is essential for catalysis to proceed.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Stereo view of the amino acid residues that form the NBD-binding pocket. All the residues shown lie within 5 of any atom on the NBD ring. Atoms are shown in standard colours.
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 831-837) copyright 1998.  
  Figure was 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.  
20161776 A.Grüber, M.S.Manimekalai, A.M.Balakrishna, C.Hunke, J.Jeyakanthan, P.R.Preiser, and G.Grüber (2010).
Structural determination of functional units of the nucleotide binding domain (NBD94) of the reticulocyte binding protein Py235 of Plasmodium yoelii.
  PLoS One, 5, e9146.
PDB code: 3hgf
20082212 C.Hunke, V.S.Tadwal, M.S.Manimekalai, M.Roessle, and G.Grüber (2010).
The effect of NBD-Cl in nucleotide-binding of the major subunit alpha and B of the motor proteins F1FO ATP synthase and A1AO ATP synthase.
  J Bioenerg Biomembr, 42, 1.  
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.  
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.  
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.  
18957411 J.K.Ramalingam, C.Hunke, X.Gao, G.Grüber, and P.R.Preiser (2008).
ATP/ADP Binding to a Novel Nucleotide Binding Domain of the Reticulocyte-binding Protein Py235 of Plasmodium yoelii.
  J Biol Chem, 283, 36386-36396.  
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.  
17438143 M.Boerries, P.Most, J.R.Gledhill, J.E.Walker, H.A.Katus, W.J.Koch, U.Aebi, and C.A.Schoenenberger (2007).
Ca2+ -dependent interaction of S100A1 with F1-ATPase leads to an increased ATP content in cardiomyocytes.
  Mol Cell Biol, 27, 4365-4373.  
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
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.  
16855309 T.C.Terwilliger, H.Klei, P.D.Adams, N.W.Moriarty, and J.D.Cohn (2006).
Automated ligand fitting by core-fragment fitting and extension into density.
  Acta Crystallogr D Biol Crystallogr, 62, 915-922.  
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.  
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.  
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.  
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.  
10838039 H.Ren, and W.S.Allison (2000).
On what makes the gamma subunit spin during ATP hydrolysis by F(1).
  Biochim Biophys Acta, 1458, 221-233.  
10838040 J.A.Berden, and A.F.Hartog (2000).
Analysis of the nucleotide binding sites of mitochondrial ATP synthase provides evidence for a two-site catalytic mechanism.
  Biochim Biophys Acta, 1458, 234-251.  
10819998 J.Weber, and A.E.Senior (2000).
Features of F(1)-ATPase catalytic and noncatalytic sites revealed by fluorescence lifetimes and acrylamide quenching of specifically inserted tryptophan residues.
  Biochemistry, 39, 5287-5294.  
10838046 J.Weber, and A.E.Senior (2000).
ATP synthase: what we know about ATP hydrolysis and what we do not know about ATP synthesis.
  Biochim Biophys Acta, 1458, 300-309.  
10463071 Y.Kagawa (1999).
Biophysical studies on ATP synthase.
  Adv Biophys, 36, 1.  
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.