PDBsum entry 5lqz

Hydrolase

PDB id: 5lqz

Contents

Protein chains

30 a.a.

25 a.a.

17 a.a.

27 a.a.

506 a.a.

471 a.a.

267 a.a.

128 a.a.

57 a.a.

43 a.a.

(+ 4 more) 73 a.a.

163 a.a.

154 a.a.

145 a.a.

21 a.a.

122 a.a.

44 a.a.

Ligands

ATP

ADP ×5

Metals

_MG ×5

PDB id:

5lqz

Name:

Hydrolase

Title:

Structure of f-atpase from pichia angusta, state1

Structure:

Atp synthase subunit f. Chain: 1. Atp synthase subunit aap1. Chain: 2. Atp synthase subunit a. Chain: 3. Other_details: helix 1 of subunit a. Atp synthase subunit b. Chain: 4.

Source:

Ogataea angusta. Organism_taxid: 870730. Variant: a16. Variant: a16

Authors:

K.R.Vinothkumar,M.G.Montgomery,S.Liu,J.E.Walker

Key ref:

K.R.Vinothkumar et al. (2016). Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy. Proc Natl Acad Sci U S A, 113, 12709-12714. PubMed id: 27791192

Date:

17-Aug-16 Release date: 16-Nov-16

Protein chain

No UniProt id for this chain

Struc: 30 a.a.

Protein chain

No UniProt id for this chain

Struc: 25 a.a.

Protein chain

No UniProt id for this chain

Struc: 17 a.a.

Protein chain

No UniProt id for this chain

Struc: 27 a.a.

Protein chains

W1Q6W1  (W1Q6W1_OGAPD) -  ATP synthase subunit alpha from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)

Seq: 547 a.a.

Struc: 506 a.a.*

Protein chains

W1QA59  (W1QA59_OGAPD) -  ATP synthase subunit beta from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)

Seq: 503 a.a.

Struc: 471 a.a.

Protein chain

W1QGS3  (W1QGS3_OGAPD) -  ATP synthase subunit gamma from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)

Seq: 287 a.a.

Struc: 267 a.a.*

Protein chain

W1QBD1  (W1QBD1_OGAPD) -  ATP synthase subunit delta, mitochondrial from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)

Seq: 161 a.a.

Struc: 128 a.a.*

Protein chain

No UniProt id for this chain

Struc: 57 a.a.

Protein chain

P01096  (ATIF1_BOVIN) -  ATPase inhibitor, mitochondrial from Bos taurus

Seq: 109 a.a.

Struc: 43 a.a.

Protein chains

E7E832  (E7E832_OGAPD) -  ATP synthase subunit 9, mitochondrial from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)

Seq: 76 a.a.

Struc: 73 a.a.*

Protein chain

W1QCI5  (W1QCI5_OGAPD) -  ATP synthase subunit 5, mitochondrial from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)

Seq: 205 a.a.

Struc: 163 a.a.*

Protein chain

W1Q9V2  (W1Q9V2_OGAPD) -  ATP synthase subunit 4 from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)

Seq: 231 a.a.

Struc: 154 a.a.*

Protein chain

W1Q731  (W1Q731_OGAPD) -  ATP synthase subunit d, mitochondrial from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)

Seq: 175 a.a.

Struc: 145 a.a.*

Protein chain

No UniProt id for this chain

Struc: 21 a.a.

Protein chain

E7E837  (E7E837_OGAPD) -  ATP synthase subunit a from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)

Seq: 259 a.a.

Struc: 122 a.a.*

Protein chain

No UniProt id for this chain

Struc: 44 a.a.

* PDB and UniProt seqs differ at 50 residue positions (black crosses)

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)

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

reference

Proc Natl Acad Sci U S A 113:12709-12714 (2016)

PubMed id: 27791192

Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy.

K.R.Vinothkumar, M.G.Montgomery, S.Liu, J.E.Walker.

ABSTRACT

The structure of the intact monomeric ATP synthase from the fungus, Pichia angusta, has been solved by electron cryo-microscopy. The structure provides insights into the mechanical coupling of the transmembrane proton motive force across mitochondrial membranes in the synthesis of ATP. This mechanism requires a strong and integral stator, consisting of the catalytic α₃β₃-domain, peripheral stalk, and, in the membrane domain, subunit a and associated supernumerary subunits, kept in contact with the rotor turning at speeds up to 350 Hz. The stator's integrity is ensured by robust attachment of both the oligomycin sensitivity conferral protein (OSCP) to the catalytic domain and the membrane domain of subunit b to subunit a. The ATP8 subunit provides an additional brace between the peripheral stalk and subunit a. At the junction between the OSCP and the apparently stiff, elongated α-helical b-subunit and associated d- and h-subunits, an elbow or joint allows the stator to bend to accommodate lateral movements during the activity of the catalytic domain. The stator may also apply lateral force to help keep the static a-subunit and rotating c₁₀-ring together. The interface between the c₁₀-ring and the a-subunit contains the transmembrane pathway for protons, and their passage across the membrane generates the turning of the rotor. The pathway has two half-channels containing conserved polar residues provided by a bundle of four α-helices inclined at ∼30° to the plane of the membrane, similar to those described in other species. The structure provides more insights into the workings of this amazing machine.