1fkm: Difference between revisions

Latest revision as of 08:26, 6 November 2024

CRYSTAL STRUCTURE OF THE YPT/RAB-GAP DOMAIN OF GYP1P

Structural highlights

1fkm is a 1 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 1.9Å
Ligands:	MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GYP1_YEAST Stimulates specifically the GTPase activity of YPT1. Functions on the Golgi as a negative regulator of YPT1.^[1]

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

We present the 1.9 A resolution crystal structure of the catalytic domain of Gyp1p, a specific GTPase activating protein (GAP) for Ypt proteins, the yeast homologues of Rab proteins, which are involved in vesicular transport. Gyp1p is a member of a large family of eukaryotic proteins with shared sequence motifs. Previously, no structural information was available for any member of this class of proteins. The GAP domain of Gyp1p was found to be fully alpha-helical. However, the observed fold does not superimpose with other alpha-helical GAPs (e.g. Ras- and Cdc42/Rho-GAP). The conserved and catalytically crucial arginine residue, identified by mutational analysis, is in a comparable position to the arginine finger in the Ras- and Cdc42-GAPs, suggesting that Gyp1p utilizes an arginine finger in the GAP reaction, in analogy to Ras- and Cdc42-GAPs. A model for the interaction between Gyp1p and the Ypt protein satisfying biochemical data is given.

Crystal structure of the GAP domain of Gyp1p: first insights into interaction with Ypt/Rab proteins.,Rak A, Fedorov R, Alexandrov K, Albert S, Goody RS, Gallwitz D, Scheidig AJ EMBO J. 2000 Oct 2;19(19):5105-13. PMID:11013213^[2]

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

References

↑ Du LL, Novick P. Yeast rab GTPase-activating protein Gyp1p localizes to the Golgi apparatus and is a negative regulator of Ypt1p. Mol Biol Cell. 2001 May;12(5):1215-26. PMID:11359917
↑ Rak A, Fedorov R, Alexandrov K, Albert S, Goody RS, Gallwitz D, Scheidig AJ. Crystal structure of the GAP domain of Gyp1p: first insights into interaction with Ypt/Rab proteins. EMBO J. 2000 Oct 2;19(19):5105-13. PMID:11013213 doi:10.1093/emboj/19.19.5105

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OCA

[1] Du LL, Novick P. Yeast rab GTPase-activating protein Gyp1p localizes to the Golgi apparatus and is a negative regulator of Ypt1p. Mol Biol Cell. 2001 May;12(5):1215-26. PMID:11359917

[2] Rak A, Fedorov R, Alexandrov K, Albert S, Goody RS, Gallwitz D, Scheidig AJ. Crystal structure of the GAP domain of Gyp1p: first insights into interaction with Ypt/Rab proteins. EMBO J. 2000 Oct 2;19(19):5105-13. PMID:11013213 doi:10.1093/emboj/19.19.5105

[1]

[2]

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF THE YPT/RAB-GAP DOMAIN OF GYP1P==
-<StructureSection load='1fkm' size='340' side='right' caption='[[1fkm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1fkm' size='340' side='right'caption='[[1fkm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1fkm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1fkm]] is a 1 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=1FKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FKM 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]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ek0|1ek0]]</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkm OCA], [http://pdbe.org/1fkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fkm RCSB], [http://www.ebi.ac.uk/pdbsum/1fkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1fkm ProSAT]</span></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=1fkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkm OCA], [https://pdbe.org/1fkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fkm RCSB], [https://www.ebi.ac.uk/pdbsum/1fkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fkm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GYP1_YEAST GYP1_YEAST]] Stimulates specifically the GTPase activity of YPT1. Functions on the Golgi as a negative regulator of YPT1.<ref>PMID:11359917</ref>
+[https://www.uniprot.org/uniprot/GYP1_YEAST GYP1_YEAST] Stimulates specifically the GTPase activity of YPT1. Functions on the Golgi as a negative regulator of YPT1.<ref>PMID:11359917</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fk/1fkm_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 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Albert, S]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Alexandrov, K]]
+[[Category: Albert S]]
-[[Category: Fedorov, R]]
+[[Category: Alexandrov K]]
-[[Category: Gallwitz, D]]
+[[Category: Fedorov R]]
-[[Category: Goody, R S]]
+[[Category: Gallwitz D]]
-[[Category: Rak, A]]
+[[Category: Goody RS]]
-[[Category: Scheidig, A J]]
+[[Category: Rak A]]
-[[Category: Endocytosis]]
+[[Category: Scheidig AJ]]
-[[Category: Endocytosis-exocytosis complex]]
-[[Category: Gap]]
-[[Category: Gtpase activation]]
-[[Category: Hydrolase]]
-[[Category: Vesicular trafficking]]
-[[Category: Ypt/rab protein]]

1fkm: Difference between revisions

Latest revision as of 08:26, 6 November 2024

CRYSTAL STRUCTURE OF THE YPT/RAB-GAP DOMAIN OF GYP1P

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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