1ek0

From Proteopedia

(Difference between revisions)

Revision as of 05:59, 9 August 2023

GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION

Structural highlights

1ek0 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 1.48Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VPS21_YEAST Required for protein transport to the vacuole. Involved in two vesicle trafficking steps to the prevacuolar compartment (PVC), regulating the docking of endosomes and Golgi vesicles to the PVC by interacting with PEP7/VAC1 on the PVC membrane and promoting SNARE complex formation.^[1] ^[2]

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

Ypt/Rab proteins are membrane-associated small GTP-binding proteins which play a central role in the coordination, activation and regulation of vesicle-mediated transport in eukaryotic cells. We present the 1.5 A high-resolution crystal structure of Ypt51 in its active, GppNHp-bound conformation. Ypt51 is an important regulator involved in the endocytic membrane traffic of Saccharomyces cerevisiae. The structure reveals small but significant structural differences compared with H-Ras p21. The effector loop and the catalytic loop are well defined and stabilized by extensive hydrophobic interactions. The switch I and switch II regions form a well-defined epitope for hypothetical effector protein binding. Sequence comparisons between the different isoforms Ypt51, Ypt52 and Ypt53 provide the first insights into determinants for specific effector binding and for fine-tuning of the intrinsic GTP-hydrolysis rate.

High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis.,Esters H, Alexandrov K, Constantinescu AT, Goody RS, Scheidig AJ J Mol Biol. 2000 Apr 21;298(1):111-21. PMID:10756108^[3]

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

References

↑ Gerrard SR, Bryant NJ, Stevens TH. VPS21 controls entry of endocytosed and biosynthetic proteins into the yeast prevacuolar compartment. Mol Biol Cell. 2000 Feb;11(2):613-26. PMID:10679018
↑ Horazdovsky BF, Busch GR, Emr SD. VPS21 encodes a rab5-like GTP binding protein that is required for the sorting of yeast vacuolar proteins. EMBO J. 1994 Mar 15;13(6):1297-309. PMID:8137814
↑ Esters H, Alexandrov K, Constantinescu AT, Goody RS, Scheidig AJ. High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis. J Mol Biol. 2000 Apr 21;298(1):111-21. PMID:10756108 doi:10.1006/jmbi.2000.3645

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/1ek0"

Categories: Large Structures | Saccharomyces cerevisiae | Esters H | Scheidig AJ

@@ Line 3: / Line 3: @@
 <StructureSection load='1ek0' size='340' side='right'caption='[[1ek0]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ek0]] is a 1 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=1EK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EK0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ek0]] 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=1EK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EK0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 1.48&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=1ek0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ek0 OCA], [https://pdbe.org/1ek0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ek0 RCSB], [https://www.ebi.ac.uk/pdbsum/1ek0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ek0 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/VPS21_YEAST VPS21_YEAST]] Required for protein transport to the vacuole. Involved in two vesicle trafficking steps to the prevacuolar compartment (PVC), regulating the docking of endosomes and Golgi vesicles to the PVC by interacting with PEP7/VAC1 on the PVC membrane and promoting SNARE complex formation.<ref>PMID:10679018</ref> <ref>PMID:8137814</ref>
+[https://www.uniprot.org/uniprot/VPS21_YEAST VPS21_YEAST] Required for protein transport to the vacuole. Involved in two vesicle trafficking steps to the prevacuolar compartment (PVC), regulating the docking of endosomes and Golgi vesicles to the PVC by interacting with PEP7/VAC1 on the PVC membrane and promoting SNARE complex formation.<ref>PMID:10679018</ref> <ref>PMID:8137814</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Esters, H]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Scheidig, A J]]
+[[Category: Esters H]]
-[[Category: Endocytosis]]
+[[Category: Scheidig AJ]]
-[[Category: Endocytosis-exocytosis complex]]
-[[Category: G protein]]
-[[Category: Gtp hydrolysis]]
-[[Category: Hydrolase]]
-[[Category: Vesicular traffic]]
-[[Category: Ypt/rab protein]]

1ek0

From Proteopedia

Revision as of 05:59, 9 August 2023

GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox