2zxu: Difference between revisions

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-{{Seed}}
-[[Image:2zxu.jpg|left|200px]]
-<!--
+==Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe) and DMASPP==
-The line below this paragraph, containing "STRUCTURE_2zxu", creates the "Structure Box" on the page.
+<StructureSection load='2zxu' size='340' side='right'caption='[[2zxu]], [[Resolution|resolution]] 2.75&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'>[[2zxu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZXU 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]] 2.75&#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></td></tr>
-{{STRUCTURE_2zxu|  PDB=2zxu  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxu OCA], [https://pdbe.org/2zxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zxu RCSB], [https://www.ebi.ac.uk/pdbsum/2zxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MIAA_ECOLI MIAA_ECOLI] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A).<ref>PMID:9012675</ref> <ref>PMID:9148919</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/zx/2zxu_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=2zxu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacterial and eukaryotic tRNAs that decode codons starting with uridine have a hydrophobically hypermodified adenosine at position 37 (A(37)) adjacent to the 3'-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear as to how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during the modification of RNA. A compact evolutionary inserted domain (herein swinging domain) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of the tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A(36) and A(38) together to squeeze out A(37) into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate binding of MiaA.
-===Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe) and DMASPP===
+Snapshots of Dynamics in Synthesizing N(6)-Isopentenyladenosine at the tRNA Anticodon.,Chimnaronk S, Forouhar F, Sakai J, Yao M, Tron CM, Atta M, Fontecave M, Hunt JF, Tanaka I Biochemistry. 2009 May 20. PMID:19435325<ref>PMID:19435325</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2zxu" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19435325}}, adds the Publication Abstract to the page
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19435325 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19435325}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-ZXU is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXU OCA].
+[[Category: Large Structures]]
+[[Category: Chimnaronk S]]
-==Reference==
+[[Category: Sakai J]]
-<ref group="xtra">PMID:19435325</ref><references group="xtra"/>
+[[Category: Tanaka I]]
-[[Category: Escherichia coli]]
+[[Category: Yao M]]
-[[Category: TRNA isopentenyltransferase]]
-[[Category: Chimnaronk, S.]]
-[[Category: Sakai, J.]]
-[[Category: Tanaka, I.]]
-[[Category: Yao, M.]]
-[[Category: Atp-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Protein-rna complex]]
-[[Category: Transferase]]
-[[Category: Transferase/rna complex]]
-[[Category: Trna modification enzyme]]
-[[Category: Trna processing]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 27 15:17:00 2009''