4IX9

Crystal structure of subunit F of V-ATPase from S. cerevisiae

Summary for 4IX9

• Entry DOI: 10.2210/pdb4ix9/pdb
• Descriptor: V-type proton ATPase subunit F, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, GLYCEROL, ... (4 entities in total)
• Functional Keywords: v-atpase, stalk subunit, subunit f, rossmann fold, regulatory, coupling, hydrolase
• Biological source: Saccharomyces cerevisiae (yeast)
• Total number of polymer chains: 4
• Total formula weight: 43992.14

Authors

Basak, S.,Balakrishna, A.M.,Manimekalai, M.S.S.,Gruber, G. (deposition date: 2013-01-24, release date: 2013-03-20, Last modification date: 2024-10-16)

Primary citation

Basak, S.,Lim, J.,Manimekalai, M.S.S.,Balakrishna, A.M.,Gruber, G.
Crystal and NMR structures give insights into the role and dynamics of subunit F of the eukaryotic V-ATPase from Saccharomyces cerevisiae
J.Biol.Chem., 288:11930-11939, 2013

PubMed Abstract: Subunit F of V-ATPases is proposed to undergo structural alterations during catalysis and reversible dissociation from the V1VO complex. Recently, we determined the low resolution structure of F from Saccharomyces cerevisiae V-ATPase, showing an N-terminal egg shape, connected to a C-terminal hook-like segment via a linker region. To understand the mechanistic role of subunit F of S. cerevisiae V-ATPase, composed of 118 amino acids, the crystal structure of the major part of F, F(1-94), was solved at 2.3 Å resolution. The structural features were confirmed by solution NMR spectroscopy using the entire F subunit. The eukaryotic F subunit consists of the N-terminal F(1-94) domain with four-parallel β-strands, which are intermittently surrounded by four α-helices, and the C terminus, including the α5-helix encompassing residues 103 to 113. Two loops (26)GQITPETQEK(35) and (60)ERDDI(64) are described to be essential in mechanistic processes of the V-ATPase enzyme. The (26)GQITPETQEK(35) loop becomes exposed when fitted into the recently determined EM structure of the yeast V1VO-ATPase. A mechanism is proposed in which the (26)GQITPETQEK(35) loop of subunit F and the flexible C-terminal domain of subunit H move in proximity, leading to an inhibitory effect of ATPase activity in V1. Subunits D and F are demonstrated to interact with subunit d. Together with NMR dynamics, the role of subunit F has been discussed in the light of its interactions in the processes of reversible disassembly and ATP hydrolysis of V-ATPases by transmitting movements of subunit d and H of the VO and V1 sector, respectively.

PubMed: 23476018
DOI: 10.1074/jbc.M113.461533

Experimental method

X-RAY DIFFRACTION (2.33 Å)