Longin-like folds identified in CHiPS and DUF254 proteins: Vesicle trafficking complexes conserved in eukaryotic evolution

Protein Science

Volumn 15, Issue 11, 2006, Pages 2669-2674

  Kinch, Lisa N ^a   Grishin, Nick V ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Ccz1; CHiPs domain; DUF254; Fold recognition; Hermansky Pudlak Syndrome; HPS 1; HPS 4; Longin domain; Lysosome related organelles; Mon1; SNARE like superfamily; Vesicle transport

Indexed keywords

ALPHA ADAPTIN; FUNGAL PROTEIN; GUANOSINE TRIPHOSPHATASE; PROTEIN CCZ1; PROTEIN CHIPS; PROTEIN DUF254; PROTEIN MON1; SNARE PROTEIN; SULFAMETHOXYPYRIDAZINE; SYNAPTOBREVIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CELL VACUOLE; EUKARYOTE; EVOLUTION; GENOME; MEMBRANE VESICLE; NONHUMAN; OCULAR ALBINISM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; SACCHAROMYCES CEREVISIAE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CONSERVED SEQUENCE; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GUANINE NUCLEOTIDE EXCHANGE FACTORS; HUMANS; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MONOMERIC GTP-BINDING PROTEINS; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TRANSPORT VESICLES; VESICULAR TRANSPORT PROTEINS;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 33751109759     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062419006     Document Type: Article

References (31)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32 (Database issue): D138-D141.
3. Behnia, R. and Munro, S. 2005. Organelle identity and the signposts for membrane traffic. Nature 438: 597-604.
4. Boehm, M. and Bonifacino, J.S. 2001. Adaptins: The final recount. Mol. Biol. Cell 12: 2907-2920.
5. Bonifacino, J.S. and Glick, B.S. 2004. The mechanisms of vesicle budding and fusion. Cell 116: 153-166.
6. Collins, B.M., McCoy, A.J., Kent, H.M., Evans, P.R., and Owen, D.J. 2002. Molecular architecture and functional model of the endocytic AP2 complex. Cell 109: 523-535.
7. Cottage, A., Mullan, L., Portela, M.B., Hellen, E., Carver, T., Patel, S., Vavouri, T., Elgar, G., and Edwards, Y.J. 2004. Molecular characterisation of the SAND protein family: A study based on comparative genomics, structural bioinformatics and phylogeny. Cell. Mol. Biol. Lett. 9: 739-753.
8. Cuff, J.A., Clamp, M.E., Siddiqui, A.S., Finlay, M., and Barton, G.J. 1998. JPred: A consensus secondary structure prediction server. Bioinformatics 14: 892-893.
9. Esnouf, R.M. 1999. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr. D Biol. Crystallogr. 55: 938-940.
10. Ginalski, K. and Rychlewski, L. 2003. Detection of reliable and unexpected protein fold predictions using 3D-Jury. Nucleic Acids Res. 31: 3291-3292.
11. Ginalski, K., Elofsson, A., Fischer, D., and Rychlewski, L. 2003. 3D-Jury: A simple approach to improve protein structure predictions. Bioinformatics 19: 1015-1018.
12. Ginalski, K., von Grotthuss, M., Grishin, N.V., and Rychlewski, L. 2004. Detecting distant homology with Meta-BASIC. Nucleic Acids Res. 32: W576-W581.
13. Heldwein, E.E., Macia, E., Wang, J., Yin, H.L., Kirchhausen, T., and Harrison, S.C. 2004. Crystal structure of the clathrin adaptor protein 1 core. Proc. Natl. Acad. Sci. 101: 14108-14113.
14. Hoffman-Sommer, M., Grynberg, M., Kucharczyk, R., and Rytka, J. 2005. The CHiPS Domain - Ancient traces for the Hermansky-Pudlak syndrome. Traffic 6: 534-538.
15. Katoh, K., Kuma, K., Toh, H., and Miyata, T. 2005. MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
16. Madej, T., Gibrat, J.F., and Bryant, S.H. 1995. Threading a database of protein cores. Proteins 23: 356-369.
17. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
18. Pei, J. and Grishin, N.V. 2001. AL2CO: Calculation of positional conservation in a protein sequence alignment. Bioinformatics 17: 700-712.
19. Poteryaev, D. and Spang, A. 2005. A role of SAND-family proteins in endocytosis. Biochem. Soc. Trans. 33: 606-608.
20. Rohl, C.A., Strauss, C.E., Misura, K.M., and Baker, D. 2004. Protein structure prediction using Rosetta. Methods Enzymol. 383: 66-93.
21. Rossi, V., Banfield, D.K., Vacca, M., Dietrich, L.E., Ungermann, C., D'Esposito, M., Galli, T., and Filippini, F. 2004. Longins and their longin domains: Regulated SNAREs and multifunctional SNARE regulators. Trends Biochem. Sci. 29: 682-688.
22. Sadreyev, R. and Grishin, N. 2003. COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol. 326: 317-336.
23. Schlenker, O., Hendricks, A., Sinning, I., and Wild, K. 2006. The structure of the mammalian signal recognition particle (SRP) receptor as prototype for the interaction of small GTPases with Longin domains. J. Biol. Chem. 281: 8898-8906.
24. Schwartz, T. and Blobel, G. 2003. Structural basis for the function of the β subunit of the eukaryotic signal recognition particle receptor. Cell 112: 793-803.
25. Stroupe, C., Collins, K.M., Fratti, R.A., and Wickner, W. 2006. Purification of active HOPS complex reveals its affinities for phosphoinositides and the SNARE Vam7p. EMBO J. 25: 1579-1589.
26. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., et al. 2003. The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4: 41.
27. Walker, D.R. and Koonin, E.V. 1997. SEALS: A system for easy analysis of lots of sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5: 333-339.
28. Wang, C.W., Stromhaug, P.E., Shima, J., and Klionsky, D.J. 2002. The Ccz1-Mon1 protein complex is required for the late step of multiple vacuole delivery pathways. J. Biol. Chem. 277: 47917-47927.
29. Wang, C.W., Stromhaug, P.E., Kauffman, E.J., Weisman, L.S., and Klionsky, D.J. 2003. Yeast homotypic vacuole fusion requires the Ccz1-Mon1 complex during the tethering/docking stage. J. Cell Biol. 163: 973-985.
30. Wei, M.L. 2006. Hermansky-Pudlak syndrome: A disease of protein trafficking and organelle function. Pigment Cell Res. 19: 19-42.
31. Wickner, W. and Haas, A. 2000. Yeast homotypic vacuole fusion: A window on organelle trafficking mechanisms. Annu. Rev. Biochem. 69: 247-275.