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==Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum==
==Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum==
<StructureSection load='3knf' size='340' side='right' caption='[[3knf]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='3knf' size='340' side='right'caption='[[3knf]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3knf]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KNF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KNF FirstGlance]. <br>
<table><tr><td colspan='2'>[[3knf]] 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=3KNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KNF FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tc5|1tc5]], [[2dbo|2dbo]], [[1jke|1jke]], [[1j7g|1j7g]], [[3knp|3knp]], [[3ko3|3ko3]], [[3ko4|3ko4]], [[3ko5|3ko5]], [[3ko7|3ko7]], [[3ko9|3ko9]], [[3kob|3kob]], [[3koc|3koc]], [[3kod|3kod]]</td></tr>
</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><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dtd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5833 Plasmodium falciparum])</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=3knf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3knf OCA], [https://pdbe.org/3knf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3knf RCSB], [https://www.ebi.ac.uk/pdbsum/3knf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3knf ProSAT]</span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3knf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3knf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3knf RCSB], [http://www.ebi.ac.uk/pdbsum/3knf PDBsum]</span></td></tr>
</table>
<table>
== 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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kn/3knf_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kn/3knf_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=3knf ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
D-tyrosyl-tRNA(Tyr) deacylase (DTD) is an editing enzyme that removes D-amino acids from mischarged tRNAs. We describe an in-depth analysis of the malaria parasite Plasmodium falciparum DTD here. Our data provide structural insights into DTD complexes with adenosine and D-amino acids. Bound adenosine is proximal to the DTD catalysis site, and it represents the authentic terminal adenosine of charged tRNA. DTD-bound D-amino acids cluster at three different subsites within the overall active site pocket. These subsites, called transition, active, and exit subsites allow docking, re-orientation, chiral selection, catalysis, and exit of the free D-amino acid from DTD. Our studies reveal variable modes of D-amino acid recognition by DTDs, suggesting an inherent plasticity that can accommodate all D-amino acids. An in-depth analysis of native, ADP-bound, and D-amino acid-complexed DTD structures provide the first atomic snapshots of ligand recognition and subsequent catalysis by this enzyme family. We have mapped sites for the deacylation reaction and mark possible routes for entry and egress of all substrates and products. We have also performed structure-based inhibitor discovery and tested lead compounds against the malaria parasite P. falciparum using growth inhibition assays. Our studies provide a comprehensive structural basis for the catalytic mechanism of DTD enzymes and have implications for inhibition of this enzyme in P. falciparum as a route to inhibiting the parasite.
Ligand-bound structures provide atomic snapshots for the catalytic mechanism of D-amino acid deacylase.,Bhatt TK, Yogavel M, Wydau S, Berwal R, Sharma A J Biol Chem. 2010 Feb 19;285(8):5917-30. Epub 2009 Dec 9. PMID:20007323<ref>PMID:20007323</ref>
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Plasmodium falciparum]]
[[Category: Large Structures]]
[[Category: Bhatt, T K.]]
[[Category: Plasmodium falciparum 3D7]]
[[Category: Manickam, Y.]]
[[Category: Bhatt TK]]
[[Category: Sharma, A.]]
[[Category: Manickam Y]]
[[Category: D-amino acid]]
[[Category: Sharma A]]
[[Category: Deacylase]]
[[Category: Hydrolase]]

Latest revision as of 08:29, 20 March 2024

Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum

3knf, resolution 3.00Å

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