Home LiteratureArticle Details
PMID: 23142977 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11-Å resolution.

Nature structural & molecular biology ·Vol. 19 ·No. 12 ·2012-12-00 ·Pages 1356-62

Benlekbir S, Bueler SA, Rubinstein JL

Abstract

Vacuolar-type ATPases (V-type ATPases) in eukaryotic cells are large membrane protein complexes that acidify various intracellular compartments. The enzymes are regulated by dissociation of the V(1) and V(O) regions of the complex. Here we present the structure of the Saccharomyces cerevisiae V-type ATPase at 11-Å resolution by cryo-EM of protein particles in ice. The structure explains many cross-linking and protein interaction studies. Docking of crystal structures suggests that inhibition of ATPase activity by the dissociated V(1) region involves rearrangement of the N- and C-terminal domains of subunit H and also suggests how this inhibition is triggered upon dissociation. We provide support for this model by demonstrating that mutation of subunit H to increase the rigidity of the linker between its two domains decreases its ability to inhibit ATPase activity.

MeSH Terms
Cryoelectron Microscopy Protein Conformation Saccharomyces cerevisiae/enzymology Vacuolar Proton-Translocating ATPases/chemistry,metabolism,ultrastructure
Chemicals
Vacuolar Proton-Translocating ATPases
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Benlekbir Samir
Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.
Bueler Stephanie A
Rubinstein John L
References (58)
58 references, click to expand
  1. Peripheral stator of the yeast V-ATPase: stoichiometry and specificity of interaction between the EG complex and subunits C and H.
    Biochemistry. 2005 Dec 6;44(48):15906-14 PMID: 16313193
  2. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement.
    Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W610-4 PMID: 15215461
  3. RF cloning: a restriction-free method for inserting target genes into plasmids.
    J Biochem Biophys Methods. 2006 Apr 30;67(1):67-74 PMID: 16480772
  4. Renal vacuolar H+-ATPase.
    Physiol Rev. 2004 Oct;84(4):1263-314 PMID: 15383652
  5. Ab initio resolution measurement for single particle structures.
    J Struct Biol. 2007 Jan;157(1):201-10 PMID: 17029845
  6. Multi-resolution contour-based fitting of macromolecular structures.
    J Mol Biol. 2002 Mar 29;317(3):375-84 PMID: 11922671
  7. The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase.
    Nat Struct Mol Biol. 2010 Mar;17(3):373-8 PMID: 20173764
  8. Disassembly and reassembly of the yeast vacuolar H(+)-ATPase in vivo.
    J Biol Chem. 1995 Jul 14;270(28):17025-32 PMID: 7622524
  9. Regulation of plasma membrane V-ATPase activity by dissociation of peripheral subunits.
    J Biol Chem. 1995 Mar 10;270(10):5649-53 PMID: 7890686
  10. Subunit interactions and requirements for inhibition of the yeast V1-ATPase.
    J Biol Chem. 2009 May 15;284(20):13316-13325 PMID: 19299516
  11. The ATP synthase--a splendid molecular machine.
    Annu Rev Biochem. 1997;66:717-49 PMID: 9242922
  12. Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology.
    Nat Rev Mol Cell Biol. 2007 Nov;8(11):917-29 PMID: 17912264
  13. Purification and properties of a cytosolic V1-ATPase.
    J Biol Chem. 1996 Aug 23;271(34):20908-13 PMID: 8702848
  14. Three-dimensional structure of A1A0 ATP synthase from the hyperthermophilic archaeon Pyrococcus furiosus by electron microscopy.
    J Biol Chem. 2009 Apr 10;284(15):10110-9 PMID: 19203996
  15. Function of a subunit isoforms of the V-ATPase in pH homeostasis and in vitro invasion of MDA-MB231 human breast cancer cells.
    J Biol Chem. 2009 Jun 12;284(24):16400-16408 PMID: 19366680
  16. EMAN: semiautomated software for high-resolution single-particle reconstructions.
    J Struct Biol. 1999 Dec 1;128(1):82-97 PMID: 10600563
  17. Domain characterization and interaction of the yeast vacuolar ATPase subunit C with the peripheral stator stalk subunits E and G.
    J Biol Chem. 2010 Aug 6;285(32):24654-64 PMID: 20529855
  18. Osteoclastic bone resorption by a polarized vacuolar proton pump.
    Science. 1989 Aug 25;245(4920):855-7 PMID: 2528207
  19. Topography and subunit stoichiometry of the coated vesicle proton pump.
    J Biol Chem. 1988 Jun 25;263(18):8796-802 PMID: 2897963
  20. MRC image processing programs.
    J Struct Biol. 1996 Jan-Feb;116(1):9-16 PMID: 8742717
  21. Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase.
    Nature. 2011 Dec 18;481(7380):214-8 PMID: 22178924
  22. Cryo-EM structure of the yeast ATP synthase.
    J Mol Biol. 2008 Oct 24;382(5):1256-64 PMID: 18722382
  23. Function and subunit interactions of the N-terminal domain of subunit a (Vph1p) of the yeast V-ATPase.
    J Biol Chem. 2008 Jul 11;283(28):19274-82 PMID: 18492665
  24. Structure of intact Thermus thermophilus V-ATPase by cryo-EM reveals organization of the membrane-bound V(O) motor.
    Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1367-72 PMID: 20080582
  25. Subunit H of the vacuolar (H+) ATPase inhibits ATP hydrolysis by the free V1 domain by interaction with the rotary subunit F.
    J Biol Chem. 2008 Feb 22;283(8):4512-9 PMID: 18156183
  26. Edged watershed segmentation: a semi-interactive algorithm for segmentation of low-resolution maps from electron cryomicroscopy.
    J Struct Biol. 2011 Oct;176(1):127-32 PMID: 21763426
  27. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.
    J Mol Biol. 2003 Oct 31;333(4):721-45 PMID: 14568533
  28. FREALIGN: high-resolution refinement of single particle structures.
    J Struct Biol. 2007 Jan;157(1):117-25 PMID: 16828314
  29. Host-guest study of left-handed polyproline II helix formation.
    Biochemistry. 2001 Dec 4;40(48):14376-83 PMID: 11724549
  30. Crystal structure of the cytoplasmic N-terminal domain of subunit I, a homolog of subunit a, of V-ATPase.
    J Mol Biol. 2011 Sep 9;412(1):14-21 PMID: 21787787
  31. Functional characterization of the N-terminal domain of subunit H (Vma13p) of the yeast vacuolar ATPase.
    J Biol Chem. 2008 Oct 24;283(43):29099-108 PMID: 18708638
  32. Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae.
    Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7134-9 PMID: 11416198
  33. A different conformation for EGC stator subcomplex in solution and in the assembled yeast V-ATPase: possible implications for regulatory disassembly.
    Structure. 2008 Dec 10;16(12):1789-98 PMID: 19081055
  34. The membrane sector of vacuolar H(+)-ATPase by itself is impermeable to protons.
    Acta Physiol Scand Suppl. 1992;607:41-7 PMID: 1333159
  35. Yeast V1-ATPase: affinity purification and structural features by electron microscopy.
    J Biol Chem. 2003 Nov 21;278(47):47299-306 PMID: 12960158
  36. Structure of the yeast vacuolar ATPase.
    J Biol Chem. 2008 Dec 19;283(51):35983-95 PMID: 18955482
  37. Crystal structure of yeast V-ATPase subunit C reveals its stator function.
    EMBO Rep. 2004 Dec;5(12):1148-52 PMID: 15540116
  38. Vma9p (subunit e) is an integral membrane V0 subunit of the yeast V-ATPase.
    J Biol Chem. 2006 Jun 2;281(22):15312-9 PMID: 16569636
  39. Cryo-electron microscopy of the vacuolar ATPase motor reveals its mechanical and regulatory complexity.
    J Mol Biol. 2009 Mar 6;386(4):989-99 PMID: 19244615
  40. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.
    J Struct Biol. 1996 Jan-Feb;116(1):190-9 PMID: 8742743
  41. The C-H peripheral stalk base: a novel component in V1-ATPase assembly.
    PLoS One. 2010 Sep 03;5(9):e12588 PMID: 20838636
  42. Crystal structure of A3B3 complex of V-ATPase from Thermus thermophilus.
    EMBO J. 2009 Dec 2;28(23):3771-9 PMID: 19893485
  43. Biomolecular pleiomorphism probed by spatial interpolation of coarse models.
    Bioinformatics. 2008 Nov 1;24(21):2460-6 PMID: 18757874
  44. The H subunit (Vma13p) of the yeast V-ATPase inhibits the ATPase activity of cytosolic V1 complexes.
    J Biol Chem. 2000 Jul 14;275(28):21761-7 PMID: 10781598
  45. Angle determination for side views in single particle electron microscopy.
    J Struct Biol. 2008 May;162(2):260-70 PMID: 18272396
  46. Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase.
    EMBO Rep. 2009 Nov;10(11):1228-34 PMID: 19779483
  47. Crystal structure of a central stalk subunit C and reversible association/dissociation of vacuole-type ATPase.
    Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):59-64 PMID: 14684831
  48. The long physiological reach of the yeast vacuolar H+-ATPase.
    J Bioenerg Biomembr. 2007 Dec;39(5-6):415-21 PMID: 18000744
  49. Stoichiometry and localization of the stator subunits E and G in Thermus thermophilus H+-ATPase/synthase.
    J Biol Chem. 2008 Feb 1;283(5):2595-603 PMID: 18055467
  50. ATP synthase from Saccharomyces cerevisiae: location of subunit h in the peripheral stalk region.
    J Mol Biol. 2005 Jan 21;345(3):513-20 PMID: 15581895
  51. Structural divergence of the rotary ATPases.
    Q Rev Biophys. 2011 Aug;44(3):311-56 PMID: 21426606
  52. Partial assembly of the yeast vacuolar H(+)-ATPase in mutants lacking one subunit of the enzyme.
    J Biol Chem. 1993 Aug 5;268(22):16845-51 PMID: 8344963
  53. VMA11 and VMA16 encode second and third proteolipid subunits of the Saccharomyces cerevisiae vacuolar membrane H+-ATPase.
    J Biol Chem. 1997 Feb 21;272(8):4795-803 PMID: 9030535
  54. Three-dimensional structure of the vacuolar ATPase. Localization of subunit H by difference imaging and chemical cross-linking.
    J Biol Chem. 2004 Oct 1;279(40):41942-9 PMID: 15269204
  55. Structure of the mitochondrial ATP synthase by electron cryomicroscopy.
    EMBO J. 2003 Dec 1;22(23):6182-92 PMID: 14633978
  56. Structure of the rotor of the V-Type Na+-ATPase from Enterococcus hirae.
    Science. 2005 Apr 29;308(5722):654-9 PMID: 15802565
  57. Visualizing density maps with UCSF Chimera.
    J Struct Biol. 2007 Jan;157(1):281-7 PMID: 16963278
  58. Inhibition of host vacuolar H+-ATPase activity by a Legionella pneumophila effector.
    PLoS Pathog. 2010 Mar 19;6(3):e1000822 PMID: 20333253
Article Info
Journal
Nature structural & molecular biology
Abbr.
Nat Struct Mol Biol
ISSN
1545-9985
DOI
10.1038/nsmb.2422
Published
2012-12-00
Epub
2012-00-11
Pages
1356-62
Language
English
Region
United States
NLM ID
101186374
Subset
IM
Grants
Canadian Institutes of Health Research · MOP 81294 · Canada
External Links
PubMed source DOI: 10.1038/nsmb.2422 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2