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PDBsum entry 3i4l

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protein ligands links
Hydrolase PDB id
3i4l
Jmol
Contents
Protein chain
524 a.a. *
Ligands
ANP
MPD ×3
ACY
TRS
Waters ×352
* Residue conservation analysis
PDB id:
3i4l
Name: Hydrolase
Title: Structural characterization for the nucleotide binding abili subunit a with amp-pnp of the a1ao atp synthase
Structure: A-type atp synthase catalytic subunit a. Chain: a. Fragment: unp residues 1-240, 617-964. Synonym: v-type atp synthase alpha chain, v-atpase subunit engineered: yes. Mutation: yes
Source: Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.221     R-free:   0.249
Authors: S.M.S.Manimekalai,A.Kumar,A.M.Balakrishna,J.Jeyakanthan,G.Gr
Key ref: A.Kumar et al. (2010). Nucleotide binding states of subunit A of the A-ATP synthase and the implication of P-loop switch in evolution. J Mol Biol, 396, 301-320. PubMed id: 19944110 DOI: 10.1016/j.jmb.2009.11.046
Date:
01-Jul-09     Release date:   12-Jan-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O57728  (VATA_PYRHO) -  V-type ATP synthase alpha chain
Seq:
Struc:
 
Seq:
Struc:
964 a.a.
524 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: 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
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ 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  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2009.11.046 J Mol Biol 396:301-320 (2010)
PubMed id: 19944110  
 
 
Nucleotide binding states of subunit A of the A-ATP synthase and the implication of P-loop switch in evolution.
A.Kumar, M.S.Manimekalai, A.M.Balakrishna, J.Jeyakanthan, G.Grüber.
 
  ABSTRACT  
 
The crystal structures of the nucleotide-empty (A(E)), 5'-adenylyl-beta,gamma-imidodiphosphate (A(PNP))-bound, and ADP (A(DP))-bound forms of the catalytic A subunit of the energy producer A(1)A(O) ATP synthase from Pyrococcus horikoshii OT3 have been solved at 2.47 A and 2.4 A resolutions. The structures provide novel features of nucleotide binding and depict the residues involved in the catalysis of the A subunit. In the A(E) form, the phosphate analog SO(4)(2-) binds, via a water molecule, to the phosphate binding loop (P-loop) residue Ser238, which is also involved in the phosphate binding of ADP and 5'-adenylyl-beta,gamma-imidodiphosphate. Together with amino acids Gly234 and Phe236, the serine residue stabilizes the arched P-loop conformation of subunit A, as shown by the 2.4-A structure of the mutant protein S238A in which the P-loop flips into a relaxed state, comparable to the one in catalytic beta subunits of F(1)F(O) ATP synthases. Superposition of the existing P-loop structures of ATPases emphasizes the unique P-loop in subunit A, which is also discussed in the light of an evolutionary P-loop switch in related A(1)A(O) ATP synthases, F(1)F(O) ATP synthases, and vacuolar ATPases and implicates diverse catalytic mechanisms inside these biological motors.
 

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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