3epk: Difference between revisions

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-[[Image:3epk.png|left|200px]]
-{{STRUCTURE_3epk|  PDB=3epk  |  SCENE=  }}
+==Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism==
+<StructureSection load='3epk' size='340' side='right'caption='[[3epk]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3epk]] is a 4 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=3EPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPK FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3epk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epk OCA], [https://pdbe.org/3epk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3epk RCSB], [https://www.ebi.ac.uk/pdbsum/3epk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3epk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MOD5_YEAST MOD5_YEAST] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).<ref>PMID:3031456</ref> <ref>PMID:10618371</ref> <ref>PMID:21873461</ref>
+== 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/ep/3epk_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=3epk ConSurf].
+<div style="clear:both"></div>
-===Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism===
+==See Also==
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-{{ABSTRACT_PUBMED_18852462}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[3epk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPK OCA].
+</StructureSection>
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:018852462</ref><references group="xtra"/>
 [[Category: Saccharomyces cerevisiae]]
-[[Category: TRNA dimethylallyltransferase]]
+[[Category: Huang RH]]
-[[Category: Huang, R H.]]
+[[Category: Zhou C]]
-[[Category: Zhou, C.]]
-[[Category: Alternative initiation]]
-[[Category: Atp-binding]]
-[[Category: Mitochondrion]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleus]]
-[[Category: Transferase]]
-[[Category: Transferase-rna complex]]
-[[Category: Trna processing]]