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PDBsum entry 1kmh

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1kmh
Jmol
Contents
Protein chains
477 a.a. *
467 a.a. *
Ligands
TTX
* Residue conservation analysis
PDB id:
1kmh
Name: Hydrolase
Title: Crystal structure of spinach chloroplast f1-atpase complexed with tentoxin
Structure: Atpase alpha subunit. Chain: a. Synonym: atp synthase alpha chain. Atpase beta subunit. Chain: b. Synonym: atp synthase beta chain. Ec: 3.6.1.34
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562. Cellular_location: chloroplast. Cellular_location: chloroplast
Biol. unit: Hexamer (from PQS)
Resolution:
3.40Å     R-factor:   0.298     R-free:   0.319
Authors: G.Groth
Key ref:
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. PubMed id: 11904410 DOI: 10.1073/pnas.052546099
Date:
16-Dec-01     Release date:   13-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06450  (ATPA_SPIOL) -  ATP synthase subunit alpha, chloroplastic
Seq:
Struc:
507 a.a.
477 a.a.
Protein chain
Pfam   ArchSchema ?
P00825  (ATPB_SPIOL) -  ATP synthase subunit beta, chloroplastic
Seq:
Struc:
498 a.a.
467 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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
+ 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   7 terms 
  Biological process     transport   7 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.052546099 Proc Natl Acad Sci U S A 99:3464-3468 (2002)
PubMed id: 11904410  
 
 
Structure of spinach chloroplast F1-ATPase complexed with the phytopathogenic inhibitor tentoxin.
G.Groth.
 
  ABSTRACT  
 
Tentoxin, a natural cyclic tetrapeptide produced by phytopathogenic fungi from the Alternaria species affects the catalytic function of the chloroplast F(1)-ATPase in certain sensitive species of plants. In this study, we show that the uncompetitive inhibitor tentoxin binds to the alphabeta-interface of the chloroplast F(1)-ATPase in a cleft localized at betaAsp-83. Most of the binding site is located on the noncatalytic alpha-subunit. The crystal structure of the tentoxin-inhibited CF(1)-complex suggests that the inhibitor is hydrogen bonded to Asp-83 in the catalytic beta-subunit but forms hydrophobic contacts with residues Ile-63, Leu-65, Val-75, Tyr-237, Leu-238, and Met-274 in the adjacent alpha-subunit. Except for minor changes around the tentoxin-binding site, the structure of the chloroplast alpha(3)beta(3)-core complex is the same as that determined with the native chloroplast ATPase. Tentoxin seems to act by inhibiting inter-subunit contacts at the alphabeta-interface and by blocking the interconversion of binding sites in the catalytic mechanism.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Location of tentoxin in the crystal structure of the chloroplast F[1]-ATPase. (A) Ribbon diagram of the structure of the chloroplast -subunit (blue) and -subunit (red) at the tentoxin-binding site. The inhibitor is shown in ball-and-stick representation. Both subunits are shown with their 3-fold crystallographic axis in vertical orientation, with the binding site facing the external medium. (B) Schematic representation of the molecular structure of a single chloroplast -pair. The structure is shown from the top as it would appear on the membrane; the 3-fold axis points toward the viewer. The bound inhibitory tentoxin molecule is drawn in cpk mode.
Figure 3.
Fig. 3. Comparison of different conformational states of the bovine mitochondrial - and -subunits to the chloroplast -complex containing tentoxin. (A) Schematic representation of the peptide backbone of three different conformations of the mitochondrial - and -subunits that represent different states of the catalytic cycle (12, 30). Both subunits were superimposed on their C[ ]-atoms. The [E], [DP], and [TP] states of the noncatalytic -subunit is shown in gray, the closed conformation of the catalytic -subunit ( [DP] and [TP]) is drawn in red, and the open [E]state is coloured in green. Positions of residues Arg-304 and Glu-67, equivalent to residues Arg-297 and Asp-83 that are arrested by the tentoxin molecule in the chloroplast structure (B), are indicated by red and black arrows, respectively. As indicated by the arrow on the right (A), a shift form the closed to the open conformation of the catalytic -subunit which occurs during the catalytic cycle is associated with a domain movement that involves the -interface at Arg-304- Glu-67.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19423706 M.Vollmar, D.Schlieper, M.Winn, C.Büchner, and G.Groth (2009).
Structure of the c14 rotor ring of the proton translocating chloroplast ATP synthase.
  J Biol Chem, 284, 18228-18235.
PDB code: 2w5j
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.  
17237797 R.Zarivach, M.Vuckovic, W.Deng, B.B.Finlay, and N.C.Strynadka (2007).
Structural analysis of a prototypical ATPase from the type III secretion system.
  Nat Struct Mol Biol, 14, 131-137.
PDB codes: 2obl 2obm
15255774 C.Mavroidis, A.Dubey, and M.L.Yarmush (2004).
Molecular machines.
  Annu Rev Biomed Eng, 6, 363-395.  
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.