2bcg

From Proteopedia

(Difference between revisions)

Revision as of 07:48, 25 December 2014

Structure of doubly prenylated Ypt1:GDI complex

Structural highlights

2bcg is a 2 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:	, , ,
Related:	1ukv
Gene:	GDI1 (Saccharomyces cerevisiae), YPT1 (Saccharomyces cerevisiae)
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[GDI1_YEAST] Regulates the GDP/GTP exchange reaction of SEC4 by inhibiting the dissociation of GDP from it, and the subsequent binding of GTP to SEC4. Plays an essential role in the yeast secretory pathway.^[1] [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.^[2] [:]^[3] ^[4] ^[5] ^[6]

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

In eukaryotic cells Rab/Ypt GTPases represent a family of key membrane traffic controllers that associate with their targeted membranes via C-terminally conjugated geranylgeranyl groups. GDP dissociation inhibitor (GDI) is a general and essential regulator of Rab recycling that extracts prenylated Rab proteins from membranes at the end of their cycle of activity and facilitates their delivery to the donor membranes. Here, we present the structure of a complex between GDI and a doubly prenylated Rab protein. We show that one geranylgeranyl residue is deeply buried in a hydrophobic pocket formed by domain II of GDI, whereas the other lipid is more exposed to solvent and is skewed across several atoms of the first moiety. Based on structural information and biophysical measurements, we propose mechanistic and thermodynamic models for GDI and Rab escort protein-mediated interaction of RabGTPase with intracellular membranes.

Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling.,Pylypenko O, Rak A, Durek T, Kushnir S, Dursina BE, Thomae NH, Constantinescu AT, Brunsveld L, Watzke A, Waldmann H, Goody RS, Alexandrov K EMBO J. 2006 Jan 11;25(1):13-23. Epub 2006 Jan 5. PMID:16395334^[7]

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

References

↑ Garrett MD, Zahner JE, Cheney CM, Novick PJ. GDI1 encodes a GDP dissociation inhibitor that plays an essential role in the yeast secretory pathway. EMBO J. 1994 Apr 1;13(7):1718-28. PMID:8157010
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ Pylypenko O, Rak A, Durek T, Kushnir S, Dursina BE, Thomae NH, Constantinescu AT, Brunsveld L, Watzke A, Waldmann H, Goody RS, Alexandrov K. Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling. EMBO J. 2006 Jan 11;25(1):13-23. Epub 2006 Jan 5. PMID:16395334

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2bcg"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2bcg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BCG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BCG FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GER:GERAN-8-YL+GERAN'>GER</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GER:GERAN-8-YL+GERAN'>GER</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ukv|1ukv]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ukv|1ukv]]</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GDI1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), YPT1 ([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">GDI1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), YPT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bcg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bcg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bcg RCSB], [http://www.ebi.ac.uk/pdbsum/2bcg 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=2bcg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bcg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bcg RCSB], [http://www.ebi.ac.uk/pdbsum/2bcg PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/GDI1_YEAST GDI1_YEAST]] Regulates the GDP/GTP exchange reaction of SEC4 by inhibiting the dissociation of GDP from it, and the subsequent binding of GTP to SEC4. Plays an essential role in the yeast secretory pathway.<ref>PMID:8157010</ref>  [[http://www.uniprot.org/uniprot/YPT1_YEAST 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.<ref>PMID:3286011</ref> [:]<ref>PMID:11879636</ref> <ref>PMID:12189143</ref> <ref>PMID:12802060</ref> <ref>PMID:15082776</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 36: @@
 </StructureSection>
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Alexandrov, K.]]
+[[Category: Alexandrov, K]]
-[[Category: Pylypenko, O.]]
+[[Category: Pylypenko, O]]
-[[Category: Rak, A.]]
+[[Category: Rak, A]]
 [[Category: Geranylgeranylation]]
 [[Category: Protein transport]]
 [[Category: Rabgtpase]]
 [[Category: Vesicular transport]]

2bcg

From Proteopedia

Revision as of 07:48, 25 December 2014

Structure of doubly prenylated Ypt1:GDI complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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