PDBsum entry 6vqb

Proton transport

PDB id: 6vqb

Contents

Protein chains

600 a.a.

459 a.a.

109 a.a.

161 a.a.

47 a.a.

232 a.a.

212 a.a.

Ligands

ADP

PDB id:

6vqb

Name:

Proton transport

Title:

Mammalian v-atpase from rat brain soluble v1 region rotational state 2 with sidk and adp (from focused refinement)

Structure:

Atpase h+-transporting v1 subunit a. Chain: a, b, c. Synonym: rcg52629. V-type proton atpase subunit b, brain isoform. Chain: d, e, f. Synonym: v-atpase subunit b 2,endomembrane proton pump 58 kda subunit,vacuolar proton pump subunit b 2. Atpase h+-transporting v1 subunit d. Chain: h.

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Legionella pneumophila subsp. Pneumophila (strain philadelphia 1 / atcc 33152 / dsm 7513). Organism_taxid: 272624. Strain: philadelphia 1 / atcc 33152 / dsm 7513. Gene: lpg0968. Expressed in: escherichia coli.

Authors:

Y.M.Abbas,J.L.Rubinstein

Key ref:

Y.M.Abbas et al. (2020). Structure of V-ATPase from the mammalian brain. Science, 367, 1240-1246. PubMed id: 32165585 DOI: 10.1126/science.aaz2924

Date:

04-Feb-20 Release date: 18-Mar-20

Protein chains

D4A133  (D4A133_RAT) -  V-type proton ATPase catalytic subunit A from Rattus norvegicus

Seq: 647 a.a.

Struc: 600 a.a.

Protein chains

P62815  (VATB2_RAT) -  V-type proton ATPase subunit B, brain isoform from Rattus norvegicus

Seq: 511 a.a.

Struc: 459 a.a.

Protein chain

Q6P503  (Q6P503_RAT) -  V-type proton ATPase subunit D from Rattus norvegicus

Seq: 247 a.a.

Struc: 109 a.a.

Protein chains

Q6PCU2  (VATE1_RAT) -  V-type proton ATPase subunit E 1 from Rattus norvegicus

Seq: 226 a.a.

Struc: 161 a.a.

Protein chains

Q8R2H0  (Q8R2H0_RAT) -  V-type proton ATPase subunit G from Rattus norvegicus

Seq: 118 a.a.

Struc: 47 a.a.

Protein chains

Q5ZWW6  (Q5ZWW6_LEGPH) -  Type IV secretion protein Dot from Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

Seq: 573 a.a.

Struc: 232 a.a.

Protein chain

Q5ZWW6  (Q5ZWW6_LEGPH) -  Type IV secretion protein Dot from Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

Seq: 573 a.a.

Struc: 212 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C: 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 = ADP) corresponds exactly) + phosphate + 5 × H(+)(out)

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

reference

DOI no: 10.1126/science.aaz2924

Science 367:1240-1246 (2020)

PubMed id: 32165585

Structure of V-ATPase from the mammalian brain.

Y.M.Abbas, D.Wu, S.A.Bueler, C.V.Robinson, J.L.Rubinstein.

ABSTRACT

In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes possess numerous subunit isoforms, which complicates their analysis. We isolated homogeneous rat brain V-ATPase through its interaction with SidK, a Legionella pneumophila effector protein. Cryo-electron microscopy allowed the construction of an atomic model, defining the enzyme's ATP:proton ratio as 3:10 and revealing a homolog of yeast subunit f in the membrane region, which we tentatively identify as RNAseK. The c ring encloses the transmembrane anchors for cleaved ATP6AP1/Ac45 and ATP6AP2/PRR, the latter of which is the (pro)renin receptor that, in other contexts, is involved in both Wnt signaling and the renin-angiotensin system that regulates blood pressure. This structure shows how ATP6AP1/Ac45 and ATP6AP2/PRR enable assembly of the enzyme's catalytic and membrane regions.