Crossref journal-article
American Association for the Advancement of Science (AAAS)
Science (221)
Abstract

Ykt6p is a nonsyntaxin SNARE implicated in multiple intracellular membrane trafficking steps. Here we present the structure of the NH 2 -terminal domain of Ykt6p (Ykt6pN, residues 1 to 140). The structure of Ykt6pN differed entirely from that of syntaxin and resembled the overall fold of the actin regulatory protein, profilin. Like some syntaxins, Ykt6p adopted a folded back conformation in which Ykt6pN bound to its COOH-terminal core domain. The NH 2 -terminal domain plays an important biological role in the function of Ykt6p, which in vitro studies revealed to include influencing the kinetics and proper assembly of SNARE complexes.

Bibliography

Tochio, H., Tsui, M. M. K., Banfield, D. K., & Zhang, M. (2001). An Autoinhibitory Mechanism for Nonsyntaxin SNARE Proteins Revealed by the Structure of Ykt6p. Science, 293(5530), 698–702.

Authors 4
  1. Hidehito Tochio (first)
  2. Marco M. K. Tsui (additional)
  3. David K. Banfield (additional)
  4. Mingjie Zhang (additional)
References 40 Referenced 117
  1. 10.1038/372055a0
  2. 10.1146/annurev.biochem.68.1.863
  3. Pelham H. R., Exp. Cell Res. 247, 1 (1999). (10.1006/excr.1998.4356) / Exp. Cell Res. by Pelham H. R. (1999)
  4. Fernandez I., et al., Cell 94, 841 (1998). (10.1016/S0092-8674(00)81742-0) / Cell by Fernandez I. (1998)
  5. Munson M., Chen X., Cocina A. E., Schultz S. M., Hughson F. M., Nature Struct. Biol. 7, 894 (2000). (10.1038/79659) / Nature Struct. Biol. by Munson M. (2000)
  6. Nicholson K. L., et al., Nature Struct. Biol. 5, 793 (1998). (10.1038/1834) / Nature Struct. Biol. by Nicholson K. L. (1998)
  7. Fiebig K. M., Rice L. M., Pollock E., Brunger A. T., Nature Struct. Biol. 6, 117 (1999). (10.1038/5803) / Nature Struct. Biol. by Fiebig K. M. (1999)
  8. Lerman J. C., Robblee J., Fairman R., Hughson F. M., Biochemistry 39, 8470 (2000). (10.1021/bi0003994) / Biochemistry by Lerman J. C. (2000)
  9. 10.1038/35006120
  10. Dulubova I., et al., EMBO J. 18, 4372 (1999). (10.1093/emboj/18.16.4372) / EMBO J. by Dulubova I. (1999)
  11. Dulubova I., Yamaguchi T., Wang Y., Südhof T. C., Rizo J., Nature Struct. Biol. 8, 258 (2001). (10.1038/85012) / Nature Struct. Biol. by Dulubova I. (2001)
  12. McNew J. A., et al., J. Biol. Chem. 272, 17776 (1997). (10.1074/jbc.272.28.17776) / J. Biol. Chem. by McNew J. A. (1997)
  13. Ungermann C., et al., J. Cell Biol. 145, 1435 (1999). (10.1083/jcb.145.7.1435) / J. Cell Biol. by Ungermann C. (1999)
  14. Tsui M. M., Banfield D. K., J. Cell Sci. 113, 145 (2000). (10.1242/jcs.113.1.145) / J. Cell Sci. by Tsui M. M. (2000)
  15. The polymerase chain reaction (PCR)–amplified NH 2 -terminal domain (residues 1 to 140 Ykt6pN) full-length Ykt6p (residues 1 to 200) and various mutants of the protein were subcloned into a modified version of pET32 vector (Novagen) termed pET32H (in which the S-tag and enterokinase cleavage encoding DNA sequences were removed). Amino acid substitutions in Ykt6p were generated by site-directed mutagenesis (27). Thioredoxin-fused His-tagged Ykt6pN was expressed in Escherichia coli BL21(DE3) cells and the fusion protein was purified by using a Ni 2+ -nitrilotriacetic acid (NTA) affinity column. The NH 2 -terminal thioredoxin His-tagged peptide fragment was cleaved by digesting the fusion protein with thrombin and Ykt6pN was purified by gel filtration. Uniformly 15 N- and 15 N/ 13 C-labeled Ykt6p proteins were prepared by growing the bacteria in M9 minimal medium containing 15 NH 4 Cl with or without 13 C 6 -glucose. NMR samples contained ∼1.0 mM of Ykt6pN in 100 mM potassium phosphate pH 6.0 5 mM d 10 -DTT (dithiothrietol) in 90% H 2 O and 10% D 2 O or 99.9% D 2 O. NMR spectra were acquired at 30°C on a Varian Inova 750-MHz spectrometer. Sequential backbone and nonaromatic nonexchangeable side-chain resonance assignments of the protein were obtained by standard heteronuclear correlation experiments (28 29). The side chains of aromatics were assigned by 1 H two-dimensional (2D) total correlation spectroscopy with nuclear Overhauser effect spectroscopy (TOCSY/NOESY) experiments of an unlabeled protein sample in D 2 O. The stereo-specific assignment of the Val and Ile methyl groups was obtained by using a 10% 13 C-labeled sample (30). Approximate interproton distance restraints were derived from NOESY spectra (a 1 H 2D homonuclear NOESY a 15 N-separated-NOESY and a 13 C-separated NOESY). NOEs were grouped into three distance ranges 1.8 to 2.7 Å (1.8 to 2.9 Å for NOEs involving NH protons) 1.8 to 3.3 Å (1.8 to 3.5 Å for NOEs involving NH protons) and 1.8 to 5.0 Å corresponding to strong medium and weak NOEs. Hydrogen bonding restraints (two per hydrogen bond where r NH-O = 1.8 to 2.2 Å and r N-O = 2.2 to 3.3 Å) were generated from the standard secondary structure of the protein on the basis of the NOE patterns and the backbone secondary chemical shifts. Backbone dihedral angle restraints (φ and ψ angles) were derived from 3 J HNα coupling constants measured by using an HNHA experiment and backbone chemical shift analysis program TALOS (31). Structures were calculated by using the program CNS (32).
  16. Mahoney N. M., Janmey P. A., Almo S. C., Nature Struct. Biol. 4, 953 (1997). (10.1038/nsb1197-953) / Nature Struct. Biol. by Mahoney N. M. (1997)
  17. Farmer B. T., et al., Nature Struct. Biol. 3, 995 (1996). (10.1038/nsb1296-995) / Nature Struct. Biol. by Farmer B. T. (1996)
  18. H. Tochio M. M. K. Tsui D. K. Banfield M. Zhang unpublished data.
  19. All yeast strains were grown at 25°C or 30°C in yeast extract–peptone–dextrose (YEPD) medium or in synthetic dextrose medium lacking the appropriate amino acids or on plates containing 5-fluoro-orotic acid (5-FOA 100 μg/ml) as appropriate. Standard yeast molecular genetic techniques were carried out as described previously (14 24). The LexA two-hybrid system was used together with the yeast reporter strain EGY48 ( MAT α his3 trp1 leu2::pLEU2-LEXAop3) and the bait (pEG202) and prey plasmids (pJG4-5) (33). The full-length fusions of Ykt6p and Phe42Glu-Ykt6p comprised residues 1 to 200 the NH 2 -domain fusion comprised residues 1 to 134 of Ykt6p and the core fusion comprised residues 136 to 200. To access the two-hybrid interaction each experiment was repeated at least three times.
  20. Yeast strains (24) were grown in YEPD for 4 hours at 30°C or for 20 hours at 12°C. Internal and secreted (external) protein samples were prepared and processed as described in (14). Equivalent amounts of internal and secreted proteins were analyzed from the wild-type and mutant strains.
  21. The (His) 6 -ykt6 (Phe42Glu) p expression construct was generated by replacing the wild-type YKT6 fragment from (His) 6 -Ykt6p with the corresponding fragment of ykt6 (encoding ykt6 (Phe42Glu) p). SNARE binding assays were performed essentially as described previously (14 24). Purified recombinant SNARE proteins were added to the washed GST-Vti1p bead slurry in a final volume of 750 μl. (His) 6 -Sed5p and (His) 6 -Tlg1p were detected by immunostaining with an antibody against His 6 (14 24) and Phe42Glu-Ykt6p was detected by immunostaining with affinity-purified Ykt6p antiserum.
  22. Band intensity was converted to arbitrary units by densitometry. The initial relative velocities at which Sed5p and Ykt6p were incorporated into the SNARE complex were determined from the slopes obtained by plotting arbitrary units against time. This was done for the data points up to and including 60 min (for Phe42Glu-Ykt6p) and 120 min (for Ykt6p) during which time the velocity was found to be constant. The relative differences in the observed velocities were expressed as a ratio of the Phe42Glu/Wild-type slopes.
  23. Supplementary material is available on Science Online at www.sciencemag.org/cgi/content/full/293/5530/698/DC1.
  24. Tsui M. M., Tai W. C. S., Banfield D. K., Mol. Biol. Cell 12, 521 (2001). (10.1091/mbc.12.3.521) / Mol. Biol. Cell by Tsui M. M. (2001)
  25. 10.1038/35025000
  26. Gonzalez L. C., Weis W. I., Scheller R. H., J. Biol. Chem. 276, 24203 (2001). (10.1074/jbc.M101584200) / J. Biol. Chem. by Gonzalez L. C. (2001)
  27. Kunkel T. A., Proc. Natl. Acad. Sci. U.S.A. 82, 488 (1985). (10.1073/pnas.82.2.488) / Proc. Natl. Acad. Sci. U.S.A. by Kunkel T. A. (1985)
  28. Bax A., Grzesiek S., Acc. Chem. Res. 26, 131 (1993). (10.1021/ar00028a001) / Acc. Chem. Res. by Bax A. (1993)
  29. Clore G. M., Gronenborn A. M., Trends Biotechnol. 16, 22 (1998). (10.1016/S0167-7799(97)01135-9) / Trends Biotechnol. by Clore G. M. (1998)
  30. Neri D., Szyperski T., Otting G., Senn H., Wuthrich K., Biochemistry 28, 7510 (1989). (10.1021/bi00445a003) / Biochemistry by Neri D. (1989)
  31. Cornilescu G., Delaglio F., Bax A., J. Biomol. NMR 13, 289 (1999). (10.1023/A:1008392405740) / J. Biomol. NMR by Cornilescu G. (1999)
  32. Brunger A. T., et al., Acta Crystallogr. D Biol. Crystallogr. 54, 905 (1998). (10.1107/S0907444998003254) / Acta Crystallogr. D Biol. Crystallogr. by Brunger A. T. (1998)
  33. E. A. Golemis J. Gyuris R. Brent Interaction Trap/Two Hybrid System to Identify Interacting Proteins (Wiley New York 1996) pp. 20.1.1–20.1.28. (10.1002/0471142301.ns0404s00)
  34. Laskowski R. A., Rullmannn J. A., MacArthur M. W., Kaptein R., Thornton J. M., J. Biomol. NMR 8, 477 (1996). (10.1007/BF00228148) / J. Biomol. NMR by Laskowski R. A. (1996)
  35. 10.1016/0263-7855(96)00009-4
  36. 10.1107/S0021889891004399
  37. Merritt E., Murphy M., Acta Crystallogr. D50, 869 (1994). / Acta Crystallogr. by Merritt E. (1994)
  38. A. Nicholls GRASP: Graphical Representation and Analysis of Surface Properties (Columbia Univ. Press New York 1992).
  39. 10.1038/26412
  40. We thank F. Hung and Q. Zhang for assistance in protein purification and gel-filtration experiments respectively and C. Rock for comments on the manuscript. This work was supported by grants from the Research Grant Council of Hong Kong to D.K.B and M.Z. and by a grant from the Human Frontiers Science Program Organization to M.Z. The NMR spectrometer used in this work was purchased with funds donated to the Biotechnology Research Institute by the Hong Kong Jockey Club. The coordinates of the structure of Ykt6pN have been deposited in the Protein Data Bank (accession code 1h8m).
Dates
Type When
Created 19 years, 5 months ago (March 28, 2006, 1:37 p.m.)
Deposited 1 year, 7 months ago (Jan. 9, 2024, 5:11 p.m.)
Indexed 2 weeks, 1 day ago (Aug. 20, 2025, 8:47 a.m.)
Issued 24 years, 1 month ago (July 27, 2001)
Published 24 years, 1 month ago (July 27, 2001)
Published Print 24 years, 1 month ago (July 27, 2001)
Funders 0

None

@article{Tochio_2001, title={An Autoinhibitory Mechanism for Nonsyntaxin SNARE Proteins Revealed by the Structure of Ykt6p}, volume={293}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1062950}, DOI={10.1126/science.1062950}, number={5530}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Tochio, Hidehito and Tsui, Marco M. K. and Banfield, David K. and Zhang, Mingjie}, year={2001}, month=jul, pages={698–702} }