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PDBsum entry 3gqb

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protein Protein-protein interface(s) links
Hydrolase PDB id
3gqb
Jmol
Contents
Protein chains
578 a.a. *
460 a.a. *
Waters ×707
* Residue conservation analysis
PDB id:
3gqb
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
Resolution:
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
Date:
24-Mar-09     Release date:   24-Nov-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q56403  (VATA_THET8) -  V-type ATP synthase alpha chain
Seq:
Struc:
 
Seq:
Struc:
578 a.a.
578 a.a.*
Protein chains
Pfam   ArchSchema ?
Q56404  (VATB_THET8) -  V-type ATP synthase beta chain
Seq:
Struc:
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.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     proton-transporting two-sector ATPase complex, catalytic domain   1 term 
  Biological process     transport   7 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
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.
 
  ABSTRACT  
 
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.  
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.