PDBsum entry 3ikj

Hydrolase

PDB id: 3ikj

Contents

Protein chain

513 a.a. *

Ligands

MPD ×3

TRS

Waters ×266

* Residue conservation analysis

PDB id:

3ikj

Name:

Hydrolase

Title:

Structural characterization for the nucleotide binding ability of subunit a mutant s238a of the a1ao atp synthase

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 subunit a. 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: 0.243 R-free: 0.304

Authors:

A.Kumar,M.S.S.Manimekali,A.M.Balakrishna,J.Jeyakanthan,G.Gruber

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

Date:

06-Aug-09 Release date: 12-Jan-10

Protein chain

O57728  (VATA_PYRHO) -  V-type ATP synthase alpha chain from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 964 a.a.

Struc: 513 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.7.1.2.2 - H(+)-transporting two-sector ATPase.
• Reaction: ATP + H2O + 4 H⁺(in) = ADP + phosphate + 5 H⁺(out)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

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.