3I4L

Structural characterization for the nucleotide binding ability of subunit A with AMP-PNP of the A1AO ATP synthase

Summary for 3I4L

• Entry DOI: 10.2210/pdb3i4l/pdb
• Related: 1VDZ 3I72 3I73
• Descriptor: A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (6 entities in total)
• Functional Keywords: hydrolase
• Biological source: Pyrococcus horikoshii; More
• Total number of polymer chains: 1
• Total formula weight: 66818.72

Authors

Manimekalai, S.M.S.,Kumar, A.,Balakrishna, A.M.,Jeyakanthan, J.,Gruber, G. (deposition date: 2009-07-01, release date: 2010-01-12, Last modification date: 2023-11-01)

Primary citation

Kumar, A.,Manimekalai, M.S.,Balakrishna, A.M.,Jeyakanthan, J.,Gruber, G.
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, 2010

PubMed 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.

PubMed: 19944110
DOI: 10.1016/j.jmb.2009.11.046

Experimental method

X-RAY DIFFRACTION (2.4 Å)