PDBsum entry 3j9v

Hydrolase

PDB id: 3j9v

Contents

Protein chains

312 a.a.

392 a.a.

210 a.a.

115 a.a.

593 a.a.

457 a.a.

345 a.a.

105 a.a.

217 a.a.

461 a.a.

(+ 4 more) 150 a.a.

PDB id:

3j9v

Name:

Hydrolase

Title:

Yeast v-atpase state 3

Structure:

V-type proton atpase subunit a, vacuolar isoform. Chain: b. Synonym: v-atpase a 1 subunit, v-atpase 95 kda subunit, vacuolar ph protein 1, vacuolar proton pump a subunit, vacuolar proton translocating atpase subunit a 1. V-type proton atpase subunit c. Chain: o. Synonym: v-atpase subunit c, v-atpase 42 kda subunit, vacuolar proton pump subunit c.

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Strain: saby31. Strain: saby31

Authors:

J.Zhao,S.Benlekbir,J.L.Rubinstein

Key ref:

J.Zhao et al. (2015). Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Nature, 521, 241-245. PubMed id: 25971514 DOI: 10.1038/nature14365

Date:

23-Feb-15 Release date: 13-May-15

Protein chain

P32563  (VPH1_YEAST) -  V-type proton ATPase subunit a, vacuolar isoform from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 840 a.a.

Struc: 312 a.a.

Protein chain

P31412  (VATC_YEAST) -  V-type proton ATPase subunit C from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 392 a.a.

Struc: 392 a.a.

Protein chain

P32610  (VATD_YEAST) -  V-type proton ATPase subunit D from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 256 a.a.

Struc: 210 a.a.

Protein chain

P39111  (VATF_YEAST) -  V-type proton ATPase subunit F from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 118 a.a.

Struc: 115 a.a.

Protein chains

P17255  (VATA_YEAST) -  V-type proton ATPase catalytic subunit A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1071 a.a.

Struc: 593 a.a.

Protein chains

P16140  (VATB_YEAST) -  V-type proton ATPase subunit B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 517 a.a.

Struc: 457 a.a.

Protein chain

P32366  (VA0D_YEAST) -  V-type proton ATPase subunit d from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 345 a.a.

Struc: 345 a.a.

Protein chains

P48836  (VATG_YEAST) -  V-type proton ATPase subunit G from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 114 a.a.

Struc: 105 a.a.

Protein chains

P22203  (VATE_YEAST) -  V-type proton ATPase subunit E from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 233 a.a.

Struc: 217 a.a.

Protein chain

P41807  (VATH_YEAST) -  V-type proton ATPase subunit H from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 478 a.a.

Struc: 461 a.a.

Protein chains

P25515  (VATL1_YEAST) -  V-type proton ATPase subunit c from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 160 a.a.

Struc: 150 a.a.

Enzyme reactions

• Enzyme class 2: Chains E, A, C: E.C.3.1.-.-
• Enzyme class 3: Chains E, A, C: E.C.7.1.2.2 - H(+)-transporting two-sector ATPase.
• Reaction: ATP + H2O + 4 H⁺(in) = ADP + phosphate + 5 H⁺(out)

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: 10.1038/nature14365

Nature 521:241-245 (2015)

PubMed id: 25971514

Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase.

J.Zhao, S.Benlekbir, J.L.Rubinstein.

ABSTRACT

Eukaryotic vacuolar H(+)-ATPases (V-ATPases) are rotary enzymes that use energy from hydrolysis of ATP to ADP to pump protons across membranes and control the pH of many intracellular compartments. ATP hydrolysis in the soluble catalytic region of the enzyme is coupled to proton translocation through the membrane-bound region by rotation of a central rotor subcomplex, with peripheral stalks preventing the entire membrane-bound region from turning with the rotor. The eukaryotic V-ATPase is the most complex rotary ATPase: it has three peripheral stalks, a hetero-oligomeric proton-conducting proteolipid ring, several subunits not found in other rotary ATPases, and is regulated by reversible dissociation of its catalytic and proton-conducting regions. Studies of ATP synthases, V-ATPases, and bacterial/archaeal V/A-ATPases have suggested that flexibility is necessary for the catalytic mechanism of rotary ATPases, but the structures of different rotational states have never been observed experimentally. Here we use electron cryomicroscopy to obtain structures for three rotational states of the V-ATPase from the yeast Saccharomyces cerevisiae. The resulting series of structures shows ten proteolipid subunits in the c-ring, setting the ATP:H(+) ratio for proton pumping by the V-ATPase at 3:10, and reveals long and highly tilted transmembrane α-helices in the a-subunit that interact with the c-ring. The three different maps reveal the conformational changes that occur to couple rotation in the symmetry-mismatched soluble catalytic region to the membrane-bound proton-translocating region. Almost all of the subunits of the enzyme undergo conformational changes during the transitions between these three rotational states. The structures of these states provide direct evidence that deformation during rotation enables the smooth transmission of power through rotary ATPases.