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3cpj

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Revision as of 10:28, 12 August 2020

Crystal structure of Ypt31 in complex with yeast Rab-GDI

Structural highlights

3cpj is a 2 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	3cph, 3cpi
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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] [YPT31_YEAST] Required for protein transport in the secretory pathway. Probably involved in regulation of secretory vesicle formation at the trans-Golgi compartment.^[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

Rab GDP dissociation inhibitors (GDI)-facilitated extraction of prenylated Rab proteins from membranes plays an important role in vesicular membrane trafficking. The investigated thermodynamic properties of yeast Rab.GDI and Rab.MRS6 complexes demonstrated differences in the Rab binding properties of the closely related Rab GDI and MRS6 proteins, consistent with their functional diversity. The importance of the Rab C terminus and its prenylation for GDI/MRS6 binding was demonstrated using both biochemical and structural data. The presented structures of the apo-form yeast Rab GDI and its two complexes with unprenylated Rab proteins, together with the earlier published structures of the prenylated Ypt1.GDI, provide evidence of allosteric regulation of the GDI lipid binding site opening, which plays a key role in the proposed mechanism of GDI-mediated Rab extraction. We suggest a model for the interaction of GDI with prenylated Rab proteins that incorporates a stepwise increase in affinity as the three different partial interactions are successively formed.

A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.,Ignatev A, Kravchenko S, Rak A, Goody RS, Pylypenko O J Biol Chem. 2008 Jun 27;283(26):18377-84. Epub 2008 Apr 20. PMID:18426803^[4]

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
↑ Benli M, Doring F, Robinson DG, Yang X, Gallwitz D. Two GTPase isoforms, Ypt31p and Ypt32p, are essential for Golgi function in yeast. EMBO J. 1996 Dec 2;15(23):6460-75. PMID:8978673
↑ Jedd G, Mulholland J, Segev N. Two new Ypt GTPases are required for exit from the yeast trans-Golgi compartment. J Cell Biol. 1997 May 5;137(3):563-80. PMID:9151665
↑ Ignatev A, Kravchenko S, Rak A, Goody RS, Pylypenko O. A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism. J Biol Chem. 2008 Jun 27;283(26):18377-84. Epub 2008 Apr 20. PMID:18426803 doi:10.1074/jbc.M709718200

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/3cpj"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Ypt31 in complex with yeast Rab-GDI==
-<StructureSection load='3cpj' size='340' side='right' caption='[[3cpj]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+<StructureSection load='3cpj' size='340' side='right'caption='[[3cpj]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3cpj]] is a 2 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=3CPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CPJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3cpj]] is a 2 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=3CPJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3CPJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3cph|3cph]], [[3cpi|3cpi]]</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=3cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cpj OCA], [http://pdbe.org/3cpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cpj RCSB], [http://www.ebi.ac.uk/pdbsum/3cpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cpj ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cpj OCA], [http://pdbe.org/3cpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cpj RCSB], [http://www.ebi.ac.uk/pdbsum/3cpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cpj ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[GTP-binding protein|GTP-binding protein]]
+*[[GTP-binding protein 3D structures|GTP-binding protein 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 37: @@
 </StructureSection>
 [[Category: Atcc 18824]]
+[[Category: Large Structures]]
 [[Category: Goody, R S]]
 [[Category: Ignatev, A]]

3cpj

From Proteopedia

Revision as of 10:28, 12 August 2020

Crystal structure of Ypt31 in complex with yeast Rab-GDI

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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