3epj: Difference between revisions

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-{{Seed}}
-[[Image:3epj.jpg|left|200px]]
-<!--
+==Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism==
-The line below this paragraph, containing "STRUCTURE_3epj", creates the "Structure Box" on the page.
+<StructureSection load='3epj' size='340' side='right'caption='[[3epj]], [[Resolution|resolution]] 3.10&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'>[[3epj]] 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=3EPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPJ 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]] 3.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3epj|  PDB=3epj  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3epj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epj OCA], [https://pdbe.org/3epj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3epj RCSB], [https://www.ebi.ac.uk/pdbsum/3epj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3epj 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/3epj_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=3epj 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)]]
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_18852462}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 18852462 is the PubMed ID number.
+</StructureSection>
--->
+[[Category: Large Structures]]
-{{ABSTRACT_PUBMED_18852462}}
-==About this Structure==
-EPJ is a [[Protein complex]] structure of sequences 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=3EPJ OCA].
-==Reference==
-Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism., Zhou C, Huang RH, Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7. Epub 2008 Oct 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18852462 18852462]
-[[Category: Protein complex]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: TRNA isopentenyltransferase]]
+[[Category: Huang RH]]
-[[Category: Huang, R H.]]
+[[Category: Zhou C]]
-[[Category: Zhou, C.]]
-[[Category: Alternative initiation]]
-[[Category: Atp-binding]]
-[[Category: Cytoplasm]]
-[[Category: Mitochondrion]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleus]]
-[[Category: Transferase]]
-[[Category: Transferase/rna complex]]
-[[Category: Trna processing]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov  5 12:59:54 2008''