Structural Basis for Rab GTPase Activation by VPS9 Domain Exchange Factors

Overview

Journal Nat Struct Mol Biol

Specialties Cell Biology
Molecular Biology

Date 2007 Apr 24

PMID 17450153

Citations 73

Authors

Anna Delprato

David G Lambright

Affiliations

Soon will be listed here.

Abstract

RABEX-5 and other exchange factors with VPS9 domains regulate endocytic trafficking through activation of the Rab family GTPases RAB5, RAB21 and RAB22. Here we report the crystal structure of the RABEX-5 catalytic core in complex with nucleotide-free RAB21, a key intermediate in the exchange reaction pathway. The structure reveals how VPS9 domain exchange factors recognize Rab GTPase substrates, accelerate GDP release and stabilize the nucleotide-free conformation. We further identify an autoinhibitory element in a predicted amphipathic helix located near the C terminus of the VPS9 domain. The autoinhibitory element overlaps with the binding site for the multivalent effector RABAPTIN-5 and potently suppresses the exchange activity of RABEX-5. Autoinhibition can be partially reversed by mutation of conserved residues on the nonpolar face of the predicted amphipathic helix or by assembly of the complex with RABAPTIN-5.

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References

Otomo A, Hadano S, Okada T, Mizumura H, Kunita R, Nishijima H . ALS2, a novel guanine nucleotide exchange factor for the small GTPase Rab5, is implicated in endosomal dynamics. Hum Mol Genet. 2003; 12(14):1671-87. DOI: 10.1093/hmg/ddg184. View

Chardin P, Camonis J, Gale N, Van Aelst L, Schlessinger J, Wigler M . Human Sos1: a guanine nucleotide exchange factor for Ras that binds to GRB2. Science. 1993; 260(5112):1338-43. DOI: 10.1126/science.8493579. View

Hama H, Tall G, Horazdovsky B . Vps9p is a guanine nucleotide exchange factor involved in vesicle-mediated vacuolar protein transport. J Biol Chem. 1999; 274(21):15284-91. DOI: 10.1074/jbc.274.21.15284. View

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View

Mattera R, Arighi C, Lodge R, Zerial M, Bonifacino J . Divalent interaction of the GGAs with the Rabaptin-5-Rabex-5 complex. EMBO J. 2002; 22(1):78-88. PMC: 140067. DOI: 10.1093/emboj/cdg015. View

Weigert R, Yeung A, Li J, Donaldson J . Rab22a regulates the recycling of membrane proteins internalized independently of clathrin. Mol Biol Cell. 2004; 15(8):3758-70. PMC: 491835. DOI: 10.1091/mbc.e04-04-0342. View

Zhu Z, DUMAS J, Lietzke S, Lambright D . A helical turn motif in Mss4 is a critical determinant of Rab binding and nucleotide release. Biochemistry. 2001; 40(10):3027-36. DOI: 10.1021/bi002680o. View

Kajiho H, Saito K, Tsujita K, Kontani K, Araki Y, Kurosu H . RIN3: a novel Rab5 GEF interacting with amphiphysin II involved in the early endocytic pathway. J Cell Sci. 2003; 116(Pt 20):4159-68. DOI: 10.1242/jcs.00718. View

Pereira-Leal J, Seabra M . Evolution of the Rab family of small GTP-binding proteins. J Mol Biol. 2001; 313(4):889-901. DOI: 10.1006/jmbi.2001.5072. View

10.

Nuoffer C, Wu S, Dascher C, Balch W . Mss4 does not function as an exchange factor for Rab in endoplasmic reticulum to Golgi transport. Mol Biol Cell. 1997; 8(7):1305-16. PMC: 276154. DOI: 10.1091/mbc.8.7.1305. View

11.

. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994; 50(Pt 5):760-3. DOI: 10.1107/S0907444994003112. View

12.

Simpson J, Griffiths G, Wessling-Resnick M, Fransen J, Bennett H, Jones A . A role for the small GTPase Rab21 in the early endocytic pathway. J Cell Sci. 2004; 117(Pt 26):6297-311. DOI: 10.1242/jcs.01560. View

13.

Khurana T, Brzostowski J, Kimmel A . A Rab21/LIM-only/CH-LIM complex regulates phagocytosis via both activating and inhibitory mechanisms. EMBO J. 2005; 24(13):2254-64. PMC: 1173156. DOI: 10.1038/sj.emboj.7600716. View

14.

Goldberg J . Structural basis for activation of ARF GTPase: mechanisms of guanine nucleotide exchange and GTP-myristoyl switching. Cell. 1998; 95(2):237-48. DOI: 10.1016/s0092-8674(00)81754-7. View

15.

Vitale G, Rybin V, Christoforidis S, Thornqvist P, McCaffrey M, Stenmark H . Distinct Rab-binding domains mediate the interaction of Rabaptin-5 with GTP-bound Rab4 and Rab5. EMBO J. 1998; 17(7):1941-51. PMC: 1170540. DOI: 10.1093/emboj/17.7.1941. View

16.

Eathiraj S, Pan X, Ritacco C, Lambright D . Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Nature. 2005; 436(7049):415-9. PMC: 1360218. DOI: 10.1038/nature03798. View

17.

Sondermann H, Soisson S, Boykevisch S, Yang S, Bar-Sagi D, Kuriyan J . Structural analysis of autoinhibition in the Ras activator Son of sevenless. Cell. 2004; 119(3):393-405. DOI: 10.1016/j.cell.2004.10.005. View

18.

Renault L, Guibert B, Cherfils J . Structural snapshots of the mechanism and inhibition of a guanine nucleotide exchange factor. Nature. 2003; 426(6966):525-30. DOI: 10.1038/nature02197. View

19.

Esters H, Alexandrov K, Iakovenko A, Ivanova T, Thoma N, Rybin V . Vps9, Rabex-5 and DSS4: proteins with weak but distinct nucleotide-exchange activities for Rab proteins. J Mol Biol. 2001; 310(1):141-56. DOI: 10.1006/jmbi.2001.4735. View

20.

Zhang X, He X, Fu X, Chang Z . Varp is a Rab21 guanine nucleotide exchange factor and regulates endosome dynamics. J Cell Sci. 2006; 119(Pt 6):1053-62. DOI: 10.1242/jcs.02810. View