PDBsum entry 3gqb

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protein Protein-protein interface(s) links
Hydrolase PDB id
Jmol PyMol
Protein chains
578 a.a. *
460 a.a. *
Waters ×707
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the a3b3 complex from v-atpase
Structure: V-type atp synthase alpha chain. Chain: a, c. Synonym: v-atpase subunit a. Engineered: yes. Mutation: yes. V-type atp synthase beta chain. Chain: b, d. Synonym: v-atpase subunit b. Engineered: yes.
Source: Thermus thermophilus hb8. Organism_taxid: 300852. Gene: atpa, ttha1273. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: atpb, ttha1272. Expression_system_taxid: 562
2.80Å     R-factor:   0.251     R-free:   0.281
Authors: M.Meher,S.Akimoto,M.Iwata,K.Nagata,Y.Hori,M.Yoshida,S.Yokoya S.Iwata,K.Yokoyama
Key ref: M.J.Maher et al. (2009). Crystal structure of A3B3 complex of V-ATPase from Thermus thermophilus. EMBO J, 28, 3771-3779. PubMed id: 19893485
24-Mar-09     Release date:   24-Nov-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q56403  (VATA_THET8) -  V-type ATP synthase alpha chain
578 a.a.
578 a.a.*
Protein chains
Pfam   ArchSchema ?
Q56404  (VATB_THET8) -  V-type ATP synthase beta chain
478 a.a.
460 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, C: E.C.  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
+ H(2)O
+ H(+)(In)
+ phosphate
+ H(+)(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transport   5 terms 
  Biochemical function     nucleotide binding     4 terms  


EMBO J 28:3771-3779 (2009)
PubMed id: 19893485  
Crystal structure of A3B3 complex of V-ATPase from Thermus thermophilus.
M.J.Maher, S.Akimoto, M.Iwata, K.Nagata, Y.Hori, M.Yoshida, S.Yokoyama, S.Iwata, K.Yokoyama.
Vacuolar-type ATPases (V-ATPases) exist in various cellular membranes of many organisms to regulate physiological processes by controlling the acidic environment. Here, we have determined the crystal structure of the A(3)B(3) subcomplex of V-ATPase at 2.8 A resolution. The overall construction of the A(3)B(3) subcomplex is significantly different from that of the alpha(3)beta(3) sub-domain in F(o)F(1)-ATP synthase, because of the presence of a protruding 'bulge' domain feature in the catalytic A subunits. The A(3)B(3) subcomplex structure provides the first molecular insight at the catalytic and non-catalytic interfaces, which was not possible in the structures of the separate subunits alone. Specifically, in the non-catalytic interface, the B subunit seems to be incapable of binding ATP, which is a marked difference from the situation indicated by the structure of the F(o)F(1)-ATP synthase. In the catalytic interface, our mutational analysis, on the basis of the A(3)B(3) structure, has highlighted the presence of a cluster composed of key hydrophobic residues, which are essential for ATP hydrolysis by V-ATPases.

Literature references that cite this PDB file's key reference

  PubMed id Reference
23334411 S.Arai, S.Saijo, K.Suzuki, K.Mizutani, Y.Kakinuma, Y.Ishizuka-Katsura, N.Ohsawa, T.Terada, M.Shirouzu, S.Yokoyama, S.Iwata, I.Yamato, and T.Murata (2013).
Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures.
  Nature, 493, 703-707.
PDB codes: 3vr2 3vr3 3vr4 3vr5 3vr6
23142977 S.Benlekbir, S.A.Bueler, and J.L.Rubinstein (2012).
Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11-Å resolution.
  Nat Struct Mol Biol, 19, 1356-1362.  
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