PDBsum entry 3mfy

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Hydrolase PDB id
Protein chain
512 a.a. *
MPD ×5
Waters ×265
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structural characterization of the subunit a mutant f236a of synthase from pyrococcus horikoshii
Structure: V-type atp synthase alpha chain. Chain: a. Fragment: catalytic subunit a (unp residues 1-240, 617-964) synonym: a-type atp synthase catalytic subunit a, v-atpase engineered: yes. Mutation: yes
Source: Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: atpa, ph1975. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.35Å     R-factor:   0.229     R-free:   0.279
Authors: A.M.Balakrishna,A.Kumar,M.S.S.Manimekali,J.Jeyakanthan,G.Gru
Key ref: A.Kumar et al. (2010). The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding. J Mol Biol, 401, 892-905. PubMed id: 20615420 DOI: 10.1016/j.jmb.2010.06.070
05-Apr-10     Release date:   07-Jul-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O57728  (VATA_PYRHO) -  V-type ATP synthase alpha chain
964 a.a.
512 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: 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!
  Cellular component     proton-transporting two-sector ATPase complex, catalytic domain   1 term 
  Biological process     proton transport   4 terms 
  Biochemical function     nucleotide binding     4 terms  


DOI no: 10.1016/j.jmb.2010.06.070 J Mol Biol 401:892-905 (2010)
PubMed id: 20615420  
The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding.
A.Kumar, M.S.Manimekalai, A.M.Balakrishna, R.Priya, G.Biuković, J.Jeyakanthan, G.Grüber.
In order to understand the residues involved in the formation of the novel arched P-loop of subunit A of the A-ATP synthase from Pyrococcus horikoshii OT3 the mutants P235A and F236A have been generated and their crystal structure were determined to resolutions of 2.38 A and 2.35 A, respectively. Both the structures show unique, altered conformations for the P-loop. Comparison with the previously solved wild type and P-loop mutant S238A structures of subunit A showed that the P-loop conformation for these two novel mutants occupy intermediate positions, with the wild type fully arched and the well relaxed S238A mutant structures taking the extreme positions. Even though the deviation is similar for both mutants the curvature of the P-loop faces opposite direction. Deviations in the GER-loop, lying above the P-loop, are similar for both mutants but in F236A it moves towards the P-loop by around 2 A. The curvature of the loop region V392-V410, located directly behind the P-loop, moves close by 3.6 A towards the P-loop in the F236A structure, and away by 2.5 A in the P235A structure. Two major deviations were observed in the P235A mutant, which are not identified in any of the subunit A structures analyzed so far. One being a wide movement of the N-terminal loop region (R90-P110) making a rotation of 80 degrees and the other is the rigid body rotation of the C-terminal helices from Q520-A588 by around 4 degrees upwards. Taken together, the data presented demonstrate the concerted effects of the critical residues P235A, F236 and S238 in the unique P-loop conformation of the A-ATP synthases.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21396943 M.S.Manimekalai, A.Kumar, J.Jeyakanthan, and G.Grüber (2011).
The transition-like state and Pi entrance into the catalytic a subunit of the biological engine A-ATP synthase.
  J Mol Biol, 408, 736-754.
PDB codes: 3nd8 3nd9 3p20
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