2e7s

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the yeast Sec2p GEF domain

Structural highlights

2e7s is a 20 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SEC2_YEAST Guanine nucleotide exchange factor for SEC4, catalyzing the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. Binds the Rab GTPase YPT32, but does not have exhange activity on YPT32.^[1] ^[2] ^[3]

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

Vesicular traffic during exocytosis is regulated by Rab GTPase, Sec4p in yeast, which is activated by a guanine nucleotide exchange factor (GEF) called Sec2p. The GEF activity is localized in the N-terminal 160 residues of Sec2p, which lacks sequence similarity with any other GEFs with known structures, and thereby the guanine nucleotide exchange mechanism by Sec2p remains unknown. Here, we report the crystal structure of the Sec2p GEF domain at 3.0 A resolution. The structure unexpectedly consists of a homodimeric, parallel coiled coil that extends over 180 A. Pull-down and guanine nucleotide exchange analyses on a series of deletion and point mutants of Sec2p unveiled the catalytic residues for its GEF activity as well as the Sec4p binding site, thus presenting a nucleotide exchange mechanism by a simple coiled coil. The present functional analyses allow us to build the Sec2p:Sec4p complex model, which explains the specificity for Rab GTPases by their respective GEF proteins.

Asymmetric coiled-coil structure with Guanine nucleotide exchange activity.,Sato Y, Shirakawa R, Horiuchi H, Dohmae N, Fukai S, Nureki O Structure. 2007 Feb;15(2):245-52. PMID:17292842^[4]

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

References

↑ Walch-Solimena C, Collins RN, Novick PJ. Sec2p mediates nucleotide exchange on Sec4p and is involved in polarized delivery of post-Golgi vesicles. J Cell Biol. 1997 Jun 30;137(7):1495-509. PMID:9199166
↑ Elkind NB, Walch-Solimena C, Novick PJ. The role of the COOH terminus of Sec2p in the transport of post-Golgi vesicles. J Cell Biol. 2000 Apr 3;149(1):95-110. PMID:10747090
↑ Ortiz D, Medkova M, Walch-Solimena C, Novick P. Ypt32 recruits the Sec4p guanine nucleotide exchange factor, Sec2p, to secretory vesicles; evidence for a Rab cascade in yeast. J Cell Biol. 2002 Jun 10;157(6):1005-15. Epub 2002 Jun 3. PMID:12045183 doi:http://dx.doi.org/10.1083/jcb.200201003
↑ Sato Y, Shirakawa R, Horiuchi H, Dohmae N, Fukai S, Nureki O. Asymmetric coiled-coil structure with Guanine nucleotide exchange activity. Structure. 2007 Feb;15(2):245-52. PMID:17292842 doi:http://dx.doi.org/10.1016/j.str.2007.01.003

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2e7s"

Categories: Large Structures | Saccharomyces cerevisiae | Fukai S | Nureki O | Sato Y

@@ Line 3: / Line 3: @@
 <StructureSection load='2e7s' size='340' side='right'caption='[[2e7s]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2e7s]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E7S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E7S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2e7s]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E7S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E7S FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e7s OCA], [https://pdbe.org/2e7s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e7s RCSB], [https://www.ebi.ac.uk/pdbsum/2e7s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e7s ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SEC2_YEAST SEC2_YEAST]] Guanine nucleotide exchange factor for SEC4, catalyzing the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. Binds the Rab GTPase YPT32, but does not have exhange activity on YPT32.<ref>PMID:9199166</ref> <ref>PMID:10747090</ref> <ref>PMID:12045183</ref>
+[https://www.uniprot.org/uniprot/SEC2_YEAST SEC2_YEAST] Guanine nucleotide exchange factor for SEC4, catalyzing the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. Binds the Rab GTPase YPT32, but does not have exhange activity on YPT32.<ref>PMID:9199166</ref> <ref>PMID:10747090</ref> <ref>PMID:12045183</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e7/2e7s_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Fukai, S]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Nureki, O]]
+[[Category: Fukai S]]
-[[Category: Sato, Y]]
+[[Category: Nureki O]]
-[[Category: Coiled coil]]
+[[Category: Sato Y]]
-[[Category: Endocytosis-exocytosis complex]]

2e7s

From Proteopedia

Current revision

Crystal structure of the yeast Sec2p GEF domain

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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