PDBsum entry 2wpd

Hydrolase

PDB id: 2wpd

Contents

Protein chains

485 a.a. *

470 a.a. *

269 a.a. *

132 a.a. *

59 a.a. *

(+ 4 more) 76 a.a. *

Ligands

ATP ×3

ADP ×2

Metals

_MG ×5

* Residue conservation analysis

PDB id:

2wpd

Name:

Hydrolase

Title:

The mg.Adp inhibited state of the yeast f1c10 atp synthase

Structure:

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

Source:

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

Resolution:

3.43Å R-factor: 0.287 R-free: 0.297

Authors:

A.Dautant,J.Velours,M.-F.Giraud

Key ref:

A.Dautant et al. (2010). Crystal structure of the Mg·ADP-inhibited state of the yeast F1c10-ATP synthase. J Biol Chem, 285, 29502-29510. PubMed id: 20610387 DOI: 10.1074/jbc.M110.124529

Date:

05-Aug-09 Release date: 07-Jul-10

Protein chains

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

Seq: 545 a.a.

Struc: 485 a.a.

Protein chains

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

Seq: 511 a.a.

Struc: 470 a.a.

Protein chain

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

Seq: 311 a.a.

Struc: 269 a.a.

Protein chain

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

Seq: 160 a.a.

Struc: 132 a.a.

Protein chain

P21306  (ATP5E_YEAST) -  ATP synthase subunit epsilon, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 62 a.a.

Struc: 59 a.a.

Protein chains

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

Seq: 76 a.a.

Struc: 76 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 (Bound ligand (Het Group name = ATP) corresponds exactly) + H2O + 4 × H(+)(in) = ADP + phosphate + 5 × H(+)(out)

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

reference

DOI no: 10.1074/jbc.M110.124529

J Biol Chem 285:29502-29510 (2010)

PubMed id: 20610387

Crystal structure of the Mg·ADP-inhibited state of the yeast F1c10-ATP synthase.

A.Dautant, J.Velours, M.F.Giraud.

ABSTRACT

The F(1)c(10) sub-complex of the yeast F(1)F(0)-ATP synthase includes the membrane rotor part c(10)-ring linked to a catalytic head (alpha/beta)(3) by a central stalk (gammadeltaepsilon). The Saccharomyces cerevisiae yF(1)c(10):ADP sub-complex was crystallized in the presence of Mg.ADP, dicyclohexylcarbodiimide (DCCD) and azide. The structure was solved by molecular replacement using a high resolution model of the yeast F(1) and a bacterial c-ring model with 10 copies of the c-subunit. The structure refined to 3.43 A resolution displays new features compared to the original yF(1)c(10) and to the yF(1) inhibited by adenylyl-imidodiphosphate (AMP-PNP) (yF(1)(I-III)). An ADP molecule was bound in both beta(DP) and beta(TP) catalytic sites. The alpha(DP)-beta (DP) pair is slightly open and resembles the novel conformation identified in yF(1) whereas the alpha (TP)-beta(TP) pair is very closed and resembles more a DP pair. yF(1)c(10) provides a model of a new Mg.ADP-inhibited state of the yeast F(1). Like for the original yF(1) and yF(1)c(10):ADP structures, the foot of the central stalk is rotated by about 40 degrees with respect to bovine structures. The assembly of the F(1) central stalk with the F(0) c-ring rotor is mainly provided by electrostatic interactions. On the rotor ring, the essential cGlu(59) carboxylate group is surrounded by hydrophobic residues and is not involved in hydrogen bonding.