3dst: Difference between revisions

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-{{Seed}}
-[[Image:3dst.png|left|200px]]
-<!--
+==Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with geranylgeranyl pyrophosphate==
-The line below this paragraph, containing "STRUCTURE_3dst", creates the "Structure Box" on the page.
+<StructureSection load='3dst' size='340' side='right'caption='[[3dst]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3dst]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DST OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DST FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GRG:GERANYLGERANYL+DIPHOSPHATE'>GRG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3dst|  PDB=3dst  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dst FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dst OCA], [https://pdbe.org/3dst PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dst RCSB], [https://www.ebi.ac.uk/pdbsum/3dst PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dst ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PGTA_RAT PGTA_RAT] Catalyzes the transfer of a geranyl-geranyl moiety from geranyl-geranyl pyrophosphate to both cysteines in Rab proteins with an -XXCC, -XCXC and -CCXX C-terminal, such as RAB1A, RAB3A and RAB5A respectively.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ds/3dst_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dst ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Post-translational isoprenylation of proteins is carried out by three related enzymes: farnesyltransferase, geranylgeranyl transferase-I, and Rab geranylgeranyl transferase (RabGGTase). Despite the fact that the last one is responsible for the largest number of individual protein prenylation events in the cell, no structural information is available on its interaction with substrates and products. Here, we present structural and biophysical analyses of RabGGTase in complex with phosphoisoprenoids as well as with the prenylated peptides that mimic the C terminus of Rab7 GTPase. The data demonstrate that, unlike other protein prenyl transferases, both RabGGTase and its substrate RabGTPases completely 'outsource' their specificity for each other to an accessory subunit, the Rab escort protein (REP). REP mediates the placement of the C terminus of RabGTPase into the active site of RabGGTase through a series protein-protein interactions of decreasing strength and selectivity. This arrangement enables RabGGTase to prenylate any cysteine-containing sequence. On the basis of our structural and thermodynamic data, we propose that RabGGTase has evolved from a GGTase-I-like molecule that 'learned' to interact with a recycling factor (GDI) that, in turn, eventually gave rise to REP.
-===Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with geranylgeranyl pyrophosphate===
+Structures of RabGGTase-substrate/product complexes provide insights into the evolution of protein prenylation.,Guo Z, Wu YW, Das D, Delon C, Cramer J, Yu S, Thuns S, Lupilova N, Waldmann H, Brunsveld L, Goody RS, Alexandrov K, Blankenfeldt W EMBO J. 2008 Sep 17;27(18):2444-56. Epub 2008 Aug 28. PMID:18756270<ref>PMID:18756270</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dst" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18756270}}, adds the Publication Abstract to the page
+*[[Geranylgeranyl transferase|Geranylgeranyl transferase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18756270 is the PubMed ID number.
+*[[Geranylgeranyl transferase 3D structures|Geranylgeranyl transferase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_18756270}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-DST is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DST OCA].
+[[Category: Large Structures]]
-==Reference==
-Structures of RabGGTase-substrate/product complexes provide insights into the evolution of protein prenylation., Guo Z, Wu YW, Das D, Delon C, Cramer J, Yu S, Thuns S, Lupilova N, Waldmann H, Brunsveld L, Goody RS, Alexandrov K, Blankenfeldt W, EMBO J. 2008 Aug 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18756270 18756270]
-[[Category: Protein complex]]
-[[Category: Protein geranylgeranyltransferase type II]]
 [[Category: Rattus norvegicus]]
-[[Category: Alexandrov, K.]]
+[[Category: Alexandrov K]]
-[[Category: Blankenfeldt, W.]]
+[[Category: Blankenfeldt W]]
-[[Category: Goody, R S.]]
+[[Category: Goody RS]]
-[[Category: Guo, Z.]]
+[[Category: Guo Z]]
-[[Category: Yu, S.]]
+[[Category: Yu S]]
-[[Category: Metal-binding]]
-[[Category: Phosphoprotein]]
-[[Category: Prenyltransferase]]
-[[Category: Protein prenylation]]
-[[Category: Transferase]]
-[[Category: Zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct  1 21:33:45 2008''