3kfu: Difference between revisions

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-{{Seed}}
-[[Image:3kfu.jpg|left|200px]]
-<!--
+==Crystal structure of the transamidosome==
-The line below this paragraph, containing "STRUCTURE_3kfu", creates the "Structure Box" on the page.
+<StructureSection load='3kfu' size='340' side='right'caption='[[3kfu]], [[Resolution|resolution]] 3.00&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'>[[3kfu]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KFU 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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3kfu|  PDB=3kfu  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kfu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kfu OCA], [https://pdbe.org/3kfu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kfu RCSB], [https://www.ebi.ac.uk/pdbsum/3kfu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kfu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GATB_THET8 GATB_THET8] Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln).
+== 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/kf/3kfu_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=3kfu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Four out of the 22 aminoacyl-tRNAs (aa-tRNAs) are systematically or alternatively synthesized by an indirect, two-step route requiring an initial mischarging of the tRNA followed by tRNA-dependent conversion of the non-cognate amino acid. During tRNA-dependent asparagine formation, tRNA(Asn) promotes assembly of a ribonucleoprotein particle called transamidosome that allows channelling of the aa-tRNA from non-discriminating aspartyl-tRNA synthetase active site to the GatCAB amidotransferase site. The crystal structure of the Thermus thermophilus transamidosome determined at 3 A resolution reveals a particle formed by two GatCABs, two dimeric ND-AspRSs and four tRNAs(Asn) molecules. In the complex, only two tRNAs are bound in a functional state, whereas the two other ones act as an RNA scaffold enabling release of the asparaginyl-tRNA(Asn) without dissociation of the complex. We propose that the crystal structure represents a transient state of the transamidation reaction. The transamidosome constitutes a transfer-ribonucleoprotein particle in which tRNAs serve the function of both substrate and structural foundation for a large molecular machine.
-===Crystal structure of the transamidosome===
+Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation.,Blaise M, Bailly M, Frechin M, Behrens MA, Fischer F, Oliveira CL, Becker HD, Pedersen JS, Thirup S, Kern D EMBO J. 2010 Sep 15;29(18):3118-29. Epub 2010 Aug 17. PMID:20717102<ref>PMID:20717102</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3kfu" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-KFU is a 14 chains structure with sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KFU OCA].
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-[[Category: Thermus thermophilus]]
+*[[Glutamyl-tRNA(Gln) amidotransferase|Glutamyl-tRNA(Gln) amidotransferase]]
-[[Category: Bailly, M.]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-[[Category: Becker, H D.]]
+== References ==
-[[Category: Blaise, M.]]
+<references/>
-[[Category: Frechin, M.]]
+__TOC__
-[[Category: Kern, D.]]
+</StructureSection>
-[[Category: Thirup, S.]]
+[[Category: Large Structures]]
-[[Category: Aminoacyl-trna synthetase]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Aspr]]
+[[Category: Bailly M]]
-[[Category: Atp-binding]]
+[[Category: Becker HD]]
-[[Category: Gatcab]]
+[[Category: Blaise M]]
-[[Category: Ligase]]
+[[Category: Frechin M]]
-[[Category: Ligase-rna complex]]
+[[Category: Kern D]]
-[[Category: Nucleotide-binding]]
+[[Category: Thirup S]]
-[[Category: Protein biosynthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:55:38 2010''