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==Crystal structure of a TRAPP subassembly activating the Rab Ypt1p==
==Crystal structure of a TRAPP subassembly activating the Rab Ypt1p==
<StructureSection load='3cue' size='340' side='right' caption='[[3cue]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
<StructureSection load='3cue' size='340' side='right' caption='[[3cue]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TRS23 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), TRS31 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), BET5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), BET3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), YPT1, YP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TRS23 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), TRS31 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), BET5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), BET3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), YPT1, YP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3cue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cue OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cue RCSB], [http://www.ebi.ac.uk/pdbsum/3cue PDBsum]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3cue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cue OCA], [http://pdbe.org/3cue PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cue RCSB], [http://www.ebi.ac.uk/pdbsum/3cue PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cue ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3cue ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 3cue" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==

Revision as of 15:50, 5 August 2016

Crystal structure of a TRAPP subassembly activating the Rab Ypt1pCrystal structure of a TRAPP subassembly activating the Rab Ypt1p

Structural highlights

3cue is a 24 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:TRS23 (Saccharomyces cerevisiae), TRS31 (Saccharomyces cerevisiae), BET5 (Saccharomyces cerevisiae), BET3 (Saccharomyces cerevisiae), YPT1, YP2 (Saccharomyces cerevisiae)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[BET3_YEAST] Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation. Required for sporulation. Has a role late in meiosis following DNA replication.[1] [2] [3] [4] [5] [TRS23_YEAST] Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation.[6] [7] [8] [BET5_YEAST] Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation. Required for sporulation. Has a role late in meiosis following DNA replication.[9] [10] [11] [12] [TRS31_YEAST] Component of the TRAPP I, TRAPP II and TRAPP III complexes which act as guanine nucleotide exchange factors (GEF) for YPT1. TRAPP I plays a key role in the late stages of endoplasmic reticulum to Golgi traffic. TRAPP II plays a role in intra-Golgi transport. TRAPP III plays a role in autophagosome formation.[13] [14] [15] [16] [YPT1_YEAST] Involved in the trafficking of secretory vesicles from the endoplasmic reticulum (ER) to the Golgi. Regulates correct targeting and tethering of vesicles to target membranes by catalyzing the selective recruitment of proteins required for tethering and fusion onto membranes. Vesicular transport depends on shuttling of YPT1 between membrane and cytosol by GDI1, probably by recycling it to its membrane of origin after a vesicle fusion event. Required for sorting and transport of proteins from the ER through the Golgi compartment. Also involved in the recycling of membrane proteins.[17] [:][18] [19] [20] [21]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The multimeric membrane-tethering complexes TRAPPI and TRAPPII share seven subunits, of which four (Bet3p, Bet5p, Trs23p, and Trs31p) are minimally needed to activate the Rab GTPase Ypt1p in an event preceding membrane fusion. Here, we present the structure of a heteropentameric TRAPPI assembly complexed with Ypt1p. We propose that TRAPPI facilitates nucleotide exchange primarily by stabilizing the nucleotide-binding pocket of Ypt1p in an open, solvent-accessible form. Bet3p, Bet5p, and Trs23p interact directly with Ypt1p to stabilize this form, while the C terminus of Bet3p invades the pocket to participate in its remodeling. The Trs31p subunit does not interact directly with the GTPase but allosterically regulates the TRAPPI interface with Ypt1p. Our findings imply that TRAPPII activates Ypt1p by an identical mechanism. This view of a multimeric membrane-tethering assembly complexed with a Rab provides a framework for understanding events preceding membrane fusion at the molecular level.

The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes.,Cai Y, Chin HF, Lazarova D, Menon S, Fu C, Cai H, Sclafani A, Rodgers DW, De La Cruz EM, Ferro-Novick S, Reinisch KM Cell. 2008 Jun 27;133(7):1202-13. PMID:18585354[22]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Rossi G, Kolstad K, Stone S, Palluault F, Ferro-Novick S. BET3 encodes a novel hydrophilic protein that acts in conjunction with yeast SNAREs. Mol Biol Cell. 1995 Dec;6(12):1769-80. PMID:8590804
  2. ↑ Sacher M, Jiang Y, Barrowman J, Scarpa A, Burston J, Zhang L, Schieltz D, Yates JR 3rd, Abeliovich H, Ferro-Novick S. TRAPP, a highly conserved novel complex on the cis-Golgi that mediates vesicle docking and fusion. EMBO J. 1998 May 1;17(9):2494-503. PMID:9564032 doi:http://dx.doi.org/10.1093/emboj/17.9.2494
  3. ↑ Sacher M, Barrowman J, Wang W, Horecka J, Zhang Y, Pypaert M, Ferro-Novick S. TRAPP I implicated in the specificity of tethering in ER-to-Golgi transport. Mol Cell. 2001 Feb;7(2):433-42. PMID:11239471
  4. ↑ Yip CK, Berscheminski J, Walz T. Molecular architecture of the TRAPPII complex and implications for vesicle tethering. Nat Struct Mol Biol. 2010 Nov;17(11):1298-304. doi: 10.1038/nsmb.1914. Epub 2010 , Oct 24. PMID:20972447 doi:http://dx.doi.org/10.1038/nsmb.1914
  5. ↑ Lynch-Day MA, Bhandari D, Menon S, Huang J, Cai H, Bartholomew CR, Brumell JH, Ferro-Novick S, Klionsky DJ. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7811-6. doi:, 10.1073/pnas.1000063107. Epub 2010 Apr 7. PMID:20375281 doi:http://dx.doi.org/10.1073/pnas.1000063107
  6. ↑ Sacher M, Barrowman J, Wang W, Horecka J, Zhang Y, Pypaert M, Ferro-Novick S. TRAPP I implicated in the specificity of tethering in ER-to-Golgi transport. Mol Cell. 2001 Feb;7(2):433-42. PMID:11239471
  7. ↑ Yip CK, Berscheminski J, Walz T. Molecular architecture of the TRAPPII complex and implications for vesicle tethering. Nat Struct Mol Biol. 2010 Nov;17(11):1298-304. doi: 10.1038/nsmb.1914. Epub 2010 , Oct 24. PMID:20972447 doi:http://dx.doi.org/10.1038/nsmb.1914
  8. ↑ Lynch-Day MA, Bhandari D, Menon S, Huang J, Cai H, Bartholomew CR, Brumell JH, Ferro-Novick S, Klionsky DJ. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7811-6. doi:, 10.1073/pnas.1000063107. Epub 2010 Apr 7. PMID:20375281 doi:http://dx.doi.org/10.1073/pnas.1000063107
  9. ↑ Jiang Y, Scarpa A, Zhang L, Stone S, Feliciano E, Ferro-Novick S. A high copy suppressor screen reveals genetic interactions between BET3 and a new gene. Evidence for a novel complex in ER-to-Golgi transport. Genetics. 1998 Jun;149(2):833-41. PMID:9611195
  10. ↑ Sacher M, Barrowman J, Wang W, Horecka J, Zhang Y, Pypaert M, Ferro-Novick S. TRAPP I implicated in the specificity of tethering in ER-to-Golgi transport. Mol Cell. 2001 Feb;7(2):433-42. PMID:11239471
  11. ↑ Yip CK, Berscheminski J, Walz T. Molecular architecture of the TRAPPII complex and implications for vesicle tethering. Nat Struct Mol Biol. 2010 Nov;17(11):1298-304. doi: 10.1038/nsmb.1914. Epub 2010 , Oct 24. PMID:20972447 doi:http://dx.doi.org/10.1038/nsmb.1914
  12. ↑ Lynch-Day MA, Bhandari D, Menon S, Huang J, Cai H, Bartholomew CR, Brumell JH, Ferro-Novick S, Klionsky DJ. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7811-6. doi:, 10.1073/pnas.1000063107. Epub 2010 Apr 7. PMID:20375281 doi:http://dx.doi.org/10.1073/pnas.1000063107
  13. ↑ Sacher M, Jiang Y, Barrowman J, Scarpa A, Burston J, Zhang L, Schieltz D, Yates JR 3rd, Abeliovich H, Ferro-Novick S. TRAPP, a highly conserved novel complex on the cis-Golgi that mediates vesicle docking and fusion. EMBO J. 1998 May 1;17(9):2494-503. PMID:9564032 doi:http://dx.doi.org/10.1093/emboj/17.9.2494
  14. ↑ Sacher M, Barrowman J, Wang W, Horecka J, Zhang Y, Pypaert M, Ferro-Novick S. TRAPP I implicated in the specificity of tethering in ER-to-Golgi transport. Mol Cell. 2001 Feb;7(2):433-42. PMID:11239471
  15. ↑ Yip CK, Berscheminski J, Walz T. Molecular architecture of the TRAPPII complex and implications for vesicle tethering. Nat Struct Mol Biol. 2010 Nov;17(11):1298-304. doi: 10.1038/nsmb.1914. Epub 2010 , Oct 24. PMID:20972447 doi:http://dx.doi.org/10.1038/nsmb.1914
  16. ↑ Lynch-Day MA, Bhandari D, Menon S, Huang J, Cai H, Bartholomew CR, Brumell JH, Ferro-Novick S, Klionsky DJ. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7811-6. doi:, 10.1073/pnas.1000063107. Epub 2010 Apr 7. PMID:20375281 doi:http://dx.doi.org/10.1073/pnas.1000063107
  17. ↑ Schmitt HD, Puzicha M, Gallwitz D. Study of a temperature-sensitive mutant of the ras-related YPT1 gene product in yeast suggests a role in the regulation of intracellular calcium. Cell. 1988 May 20;53(4):635-47. PMID:3286011
  18. ↑ Morsomme P, Riezman H. The Rab GTPase Ypt1p and tethering factors couple protein sorting at the ER to vesicle targeting to the Golgi apparatus. Dev Cell. 2002 Mar;2(3):307-17. PMID:11879636
  19. ↑ De Antoni A, Schmitzova J, Trepte HH, Gallwitz D, Albert S. Significance of GTP hydrolysis in Ypt1p-regulated endoplasmic reticulum to Golgi transport revealed by the analysis of two novel Ypt1-GAPs. J Biol Chem. 2002 Oct 25;277(43):41023-31. Epub 2002 Aug 19. PMID:12189143 doi:http://dx.doi.org/10.1074/jbc.M205783200
  20. ↑ Calero M, Chen CZ, Zhu W, Winand N, Havas KA, Gilbert PM, Burd CG, Collins RN. Dual prenylation is required for Rab protein localization and function. Mol Biol Cell. 2003 May;14(5):1852-67. Epub 2003 Feb 6. PMID:12802060 doi:10.1091/mbc.E02-11-0707
  21. ↑ Lafourcade C, Galan JM, Gloor Y, Haguenauer-Tsapis R, Peter M. The GTPase-activating enzyme Gyp1p is required for recycling of internalized membrane material by inactivation of the Rab/Ypt GTPase Ypt1p. Mol Cell Biol. 2004 May;24(9):3815-26. PMID:15082776
  22. ↑ Cai Y, Chin HF, Lazarova D, Menon S, Fu C, Cai H, Sclafani A, Rodgers DW, De La Cruz EM, Ferro-Novick S, Reinisch KM. The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes. Cell. 2008 Jun 27;133(7):1202-13. PMID:18585354 doi:10.1016/j.cell.2008.04.049

3cue, resolution 3.70Å

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