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First published online May 15, 2009
Journal of Experimental Biology 212, 1604-1610 (2009)
Published by The Company of Biologists 2009
doi: 10.1242/jeb.025866
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The little we know on the structure and machinery of V-ATPase

Shai Saroussi and Nathan Nelson*

Biochemistry Department, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel


Figure 1
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  		Fig. 1. Diagram of V-ATPase architecture. V-ATPases consist of two domains: a soluble domain, V1, and a membrane-embedded domain, Vo. F-ATPase homologous subunits are colored orange. V-ATPase unique subunits are colored light blue.

 

Figure 2
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  		Fig. 2. Diagram of subunit c from F-ATPase (A) and V-ATPase (B). Subunit c of the V-ATPase consists of four transmembrane helices, two of which are homologs of the two transmembrane helices of F-ATPase (homologous helices are colored in brown and blue). The negatively charged amino acid Asp61 of E. coli F-ATPase and Glu137 of S. cerevisiae V-ATPase (colored in red) are essential for proton translocation. The structure of subunit c from E. coli F-ATPase is according to Protein Data Bank (PDB) ID 1c0v (Grivin et al., 1998). The model of subunit c from S. cerevisiae V-ATPase was generated with 3D-JIGSAW using PDB ID 2bl2 (Murata et al., 2005Go). All structural figures were rendered with PyMOL (www.pymol.org). (C) Diagram of S. cerevisiae V-ATPase c-ring. The c-ring consists of three different subunits Vma3p, Vma11p and Vma16p (also termed c, c' and c'', respectively), which assemble a six to seven subunit ring with a possible stoichiometry of c4–5, c', c''. Subunit c' locates counterclockwise to subunit c'' (as viewed from the lumen) and the other four or five copies of subunit c complete the rest of the ring.

 

Figure 3
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  		Fig. 3. Crystal structures of V-ATPase subunits and their prokaryotic homologs. (A) Crystal structure of subunit C from S. cerevisiae (PDB ID 1U7L). The structure consists of three distinct domains. An upper globular domain, the `head' (blue). An elongated domain, the `neck' (green) and lower globular domain, the `foot' (red). (B) Crystal structure of subunit H from S. cerevisiae (PDB ID 1Ho8). There are two distinct domains. A large N-terminal domain (red) and a smaller C-terminal domain (blue). (C) Crystal structure of subunit F from T. thermophilus (PDB ID 2d00) in its `extended' form. It is elongated with two distinct domains. An N-terminal domain (red) and a C-terminal domain (blue) connected by a flexible loop (green). (D) Crystal structure of subunit B from M. mazei (PDB ID 2c61). It consists of three domains: an N-terminal domain (blue), an intermediate domain (green) and a C-terminal domain (red). A P-loop is colored yellow. (E) Crystal structure of subunit C from T. thermophilus (PDB ID 1r5z). It is funnel shaped with three similar structural domains (colored in red, green and blue). (F) Crystal structure of the K-ring from E. hire (PDB ID 2bl2). The K-ring consists of 10 identical subunits. Each subunit contains of four transmembrane {alpha}-helices (H1–4) and one soluble {alpha}-helix. Negatively charged Glu137, situated in H4 (orange stick), blocks the Na+ atom (yellow sphere). H0 is colored green, H1 is red, H2 is blue, H3 is magenta and H4 is orange.

 

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