PDBsum entry 3zry

Hydrolase

PDB id: 3zry

Contents

Protein chains

483 a.a.

471 a.a.

266 a.a.

119 a.a.

49 a.a.

(+ 4 more) 73 a.a.

Ligands

ANP ×5

Metals

_MG ×5

PDB id:

3zry

Name:

Hydrolase

Title:

Rotor architecture in the f(1)-c(10)-ring complex of the yeast f-atp synthase

Structure:

Atp synthase subunit alpha, mitochondrial. Chain: a, b, c. Atp synthase subunit beta, mitochondrial. Chain: d, e, f. Atp synthase subunit gamma, mitochondrial. Chain: g. Synonym: f-atpase gamma subunit. Atp synthase subunit delta, mitochondrial. Chain: h.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: d273-10b/a. Strain: d273-10b/a

Resolution:

6.50Å R-factor: 0.318 R-free: 0.339

Authors:

M.-F.Giraud,A.Dautant

Key ref:

M.F.Giraud et al. (2012). Rotor architecture in the yeast and bovine F1-c-ring complexes of F-ATP synthase. J Struct Biol, 177, 490-497. PubMed id: 22119846

Date:

21-Jun-11 Release date: 18-Jan-12

Protein chains

P07251  (ATPA_YEAST) -  ATP synthase subunit alpha, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 545 a.a.

Struc: 483 a.a.

Protein chains

P00830  (ATPB_YEAST) -  ATP synthase subunit beta, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 511 a.a.

Struc: 471 a.a.

Protein chain

P38077  (ATPG_YEAST) -  ATP synthase subunit gamma, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 311 a.a.

Struc: 266 a.a.

Protein chain

Q12165  (ATPD_YEAST) -  ATP synthase subunit delta, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 160 a.a.

Struc: 119 a.a.

Protein chain

E9P9X4  (E9P9X4_YEASX) -  ATP synthase catalytic sector F1 epsilon subunit from Saccharomyces cerevisiae

Seq: 62 a.a.

Struc: 49 a.a.

Protein chains

P61829  (ATP9_YEAST) -  ATP synthase subunit 9, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 76 a.a.

Struc: 73 a.a.

Enzyme reactions

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

ATP + H2O + 4 × H(+)(in) = ADP (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + phosphate + 5 × H(+)(out)

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

reference

J Struct Biol 177:490-497 (2012)

PubMed id: 22119846

Rotor architecture in the yeast and bovine F1-c-ring complexes of F-ATP synthase.

M.F.Giraud, P.Paumard, C.Sanchez, D.Brèthes, J.Velours, A.Dautant.

ABSTRACT

The F(1)F(O)-ATP synthase is a rotary molecular nanomotor. F(1) is a chemical motor driven by ATP hydrolysis while F(O) is an electrical motor driven by the proton flow. The two stepping motors are mechanically coupled through a common rotary shaft. Up to now, the three available crystal structures of the F(1)c(10) sub-complex of the yeast F(1)F(O)-ATP synthase were isomorphous and then named yF(1)c(10)(I). In this crystal form, significant interactions of the c(10)-ring with the F(1)-head of neighboring molecules affected the overall conformation of the F(1)-c-ring complex. The symmetry axis of the F(1)-head and the inertia axis of the c-ring were tilted near the interface between the F(1)-central stalk and the c-ring rotor, resulting in an unbalanced machine. We have solved a new crystal form of the F(1)c(10) complex, named yF(1)c(10)(II), inhibited by adenylyl-imidodiphosphate (AMP-PNP) and dicyclohexylcarbodiimide (DCCD), at 6.5Å resolution in which the crystal packing has a weaker influence over the conformation of the F(1)-c-ring complex. yF(1)c(10)(II) provides a model of a more efficient generator. yF(1)c(10)(II) and bovine bF(1)c(8) structures share a common rotor architecture with the inertia center of the F(1)-stator close to the rotor axis.