PDBsum entry 3fks

Hydrolase

PDB id: 3fks

Contents

Protein chains

(+ 3 more) 484 a.a. *

(+ 3 more) 466 a.a. *

268 a.a. *

116 a.a. *

46 a.a. *

235 a.a. *

68 a.a. *

25 a.a. *

187 a.a. *

11 a.a. *

25 a.a. *

Ligands

PO4 ×15

* Residue conservation analysis

PDB id:

3fks

Name:

Hydrolase

Title:

Yeast f1 atpase in the absence of bound nucleotides

Structure:

Atp synthase subunit alpha, mitochondrial. Chain: a, b, c, j, k, l, s, t, u. Fragment: unp residues 36-545. Atp synthase subunit beta, mitochondrial. Chain: d, e, f, m, n, o, v, w, x. Fragment: unp residues 34-511. Engineered: yes. Atp synthase subunit gamma, mitochondrial. Chain: g, p, y.

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Organelle: mitochondria. Gene: atp2, j2041, yjr121w. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Organelle: mitochondria

Resolution:

3.59Å R-factor: 0.244 R-free: 0.306

Authors:

V.Kabaleeswaran,J.Symersky,H.Shen,J.E.Walker,A.G.W.Leslie,D.M.Mueller

Key ref:

V.Kabaleeswaran et al. (2009). Asymmetric structure of the yeast F1 ATPase in the absence of bound nucleotides. J Biol Chem, 284, 10546-10551. PubMed id: 19233840 DOI: 10.1074/jbc.M900544200

Date:

17-Dec-08 Release date: 03-Mar-09

Protein chains

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

Seq: 545 a.a.

Struc: 484 a.a.

Protein chains

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

Seq: 511 a.a.

Struc: 466 a.a.

Protein chain

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

Seq: 311 a.a.

Struc: 268 a.a.

Protein chain

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

Seq: 160 a.a.

Struc: 116 a.a.

Protein chain

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

Seq: 62 a.a.

Struc: 46 a.a.

Protein chain

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

Seq: 311 a.a.

Struc: 235 a.a.

Protein chain

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

Seq: 160 a.a.

Struc: 68 a.a.

Protein chain

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

Seq: 62 a.a.

Struc: 25 a.a.

Protein chain

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

Seq: 311 a.a.

Struc: 187 a.a.

Protein chain

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

Seq: 160 a.a.

Struc: 11 a.a.

Protein chain

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

Seq: 62 a.a.

Struc: 25 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B, C, G, H, I, J, K, L, P, Q, R, S, T, U, Y, Z, 1: E.C.3.6.3.14 - Transferred entry: 7.1.2.2.
• Reaction: ATP + H₂O + H⁺(In) = ADP + phosphate + H⁺(Out)

ATP + H(2)O + H(+)(In) = ADP + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) + H(+)(Out)

• Enzyme class 3: Chains D, E, F, M, N, O, V, W, X: 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 + phosphate + 5 × H(+)(out) (Bound ligand (Het Group name = PO4) corresponds exactly)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.M900544200

J Biol Chem 284:10546-10551 (2009)

PubMed id: 19233840

Asymmetric structure of the yeast F1 ATPase in the absence of bound nucleotides.

V.Kabaleeswaran, H.Shen, J.Symersky, J.E.Walker, A.G.Leslie, D.M.Mueller.

ABSTRACT

The crystal structure of nucleotide-free yeast F(1) ATPase has been determined at a resolution of 3.6 A. The overall structure is very similar to that of the ground state enzyme. In particular, the beta(DP) and beta(TP) subunits both adopt the closed conformation found in the ground state structure despite the absence of bound nucleotides. This implies that interactions between the gamma and beta subunits are as important as nucleotide occupancy in determining the conformational state of the beta subunits. Furthermore, this result suggests that for the mitochondrial enzyme, there is no state of nucleotide occupancy that would result in more than one of the beta subunits adopting the open conformation. The adenine-binding pocket of the beta(TP) subunit is disrupted in the apoenzyme, suggesting that the beta(DP) subunit is responsible for unisite catalytic activity.

Selected figure(s)

Figure 1.
Electron density at the catalytic sites of yeast F[1] ATPase in the absence of nucleotides. In each panel, the 2F[o] - F[c] map is shown (contoured at 1 σ) with the position of the nucleotide modeled from the ground state structure. The inset plots show the region where the nucleotide would bind and corresponding electron density. The main chain is represented as a ribbon in red and blue for the α and β subunits, respectively. The side chains of selected residues important for substrate binding and catalysis are shown. A, α[DP]/β[DP] site; B, α[TP]/β[TP] site; C, a noncatalytic (NC) site, all for Complex I. D, the phosphate-binding site in the α[E]/β[E] site of Complex II.

Figure 3.
Electron density maps calculated with regions of the model omitted. Stereo images showing the electron density omit maps calculated excluding residues βVal-371–Leu-391 (A) and βSer-340–Pro-350, and βGlu-422–Pro-428 (B) along with the pertinent regions of the final model are shown. The 2F[o] - F[c] maps are contoured at 1 σ.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 10546-10551) copyright 2009.

Figures were selected by an automated process.