3ko3: Difference between revisions

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{{Seed}}
[[Image:3ko3.png|left|200px]]


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==D-tyrosyl-tRNA(Tyr) deacylase from Plasmodium falciparum incomplex with ADP, obtained through soaking native enzyme crystal with the ATP==
The line below this paragraph, containing "STRUCTURE_3ko3", creates the "Structure Box" on the page.
<StructureSection load='3ko3' size='340' side='right'caption='[[3ko3]], [[Resolution|resolution]] 2.80&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'>[[3ko3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum_3D7 Plasmodium falciparum 3D7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KO3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KO3 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]] 2.8&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
{{STRUCTURE_3ko3|  PDB=3ko3  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ko3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ko3 OCA], [https://pdbe.org/3ko3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ko3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ko3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ko3 ProSAT]</span></td></tr>
 
</table>
===D-tyrosyl-tRNA(Tyr) deacylase from Plasmodium falciparum incomplex with ADP, obtained through soaking native enzyme crystal with the ATP===
== Function ==
 
[https://www.uniprot.org/uniprot/DTD_PLAF7 DTD_PLAF7] D-aminoacyl-tRNA deacylase, with no observable activity on tRNAs charged with their cognate L-amino acid (PubMed:20007323, PubMed:24302572, PubMed:27224426). Probably acts by rejecting L-amino acids from its binding site rather than specific recognition of D-amino acids (PubMed:27224426). Catalyzes the hydrolysis of D-tyrosyl-tRNA(Tyr), has no activity on correctly charged L-tyrosyl-tRNA(Tyr) (PubMed:20007323, PubMed:24302572, PubMed:27224426). Hydrolyzes correctly charged, achiral, glycyl-tRNA(Gly) (PubMed:27224426). Deacylates mischarged D.melanogaster and E.coli glycyl-tRNA(Ala) (PubMed:28362257). Probably acts via tRNA-based rather than protein-based catalysis (PubMed:24302572, PubMed:27224426). Acts on tRNAs only when the D-amino acid is either attached to the ribose 3'-OH or transferred to the 3'-OH from the 2'-OH through rapid transesterification (PubMed:24302572). Binds a number of other D-amino acids (D-Arg, D-Glu, D-His, D-Lys, D-Ser), suggesting it may also deacylate other mischarged tRNAs (PubMed:20007323).<ref>PMID:20007323</ref> <ref>PMID:24302572</ref> <ref>PMID:27224426</ref> <ref>PMID:28362257</ref>
 
== Evolutionary Conservation ==
==About this Structure==
[[Image:Consurf_key_small.gif|200px|right]]
3KO3 is a 6 chains structure with sequences from [http://en.wikipedia.org/wiki/Plasmodium_falciparum_3d7 Plasmodium falciparum 3d7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KO3 OCA].  
Check<jmol>
[[Category: Plasmodium falciparum 3d7]]
  <jmolCheckbox>
[[Category: Bhatt, T K.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ko/3ko3_consurf.spt"</scriptWhenChecked>
[[Category: Manickam, Y.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Sharma, A.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: Adp]]
  </jmolCheckbox>
[[Category: Deacylase]]
</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=3ko3 ConSurf].
[[Category: Dtd]]
<div style="clear:both"></div>
[[Category: Hydrolase]]
== References ==
 
<references/>
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:49:39 2010''
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Plasmodium falciparum 3D7]]
[[Category: Bhatt TK]]
[[Category: Manickam Y]]
[[Category: Sharma A]]
Retrieved from "https://proteopedia.org/3ko3"