3ko7: Difference between revisions

Latest revision as of 08:30, 20 March 2024

DTD from Plasmodium falciparum in complex with D-Lysine

Structural highlights

3ko7 is a 6 chain structure with sequence from Plasmodium falciparum 3D7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.21Å
Ligands:	DLY
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Bhatt TK, Yogavel M, Wydau S, Berwal R, Sharma A. Ligand-bound structures provide atomic snapshots for the catalytic mechanism of D-amino acid deacylase. J Biol Chem. 2010 Feb 19;285(8):5917-30. Epub 2009 Dec 9. PMID:20007323 doi:10.1074/jbc.M109.038562
↑ Ahmad S, Routh SB, Kamarthapu V, Chalissery J, Muthukumar S, Hussain T, Kruparani SP, Deshmukh MV, Sankaranarayanan R. Mechanism of chiral proofreading during translation of the genetic code. Elife. 2013 Dec 3;2(0):e01519. doi: 10.7554/eLife.01519. PMID:24302572 doi:https://dx.doi.org/10.7554/eLife.01519
↑ Routh SB, Pawar KI, Ahmad S, Singh S, Suma K, Kumar M, Kuncha SK, Yadav K, Kruparani SP, Sankaranarayanan R. Elongation Factor Tu Prevents Misediting of Gly-tRNA(Gly) Caused by the Design Behind the Chiral Proofreading Site of D-Aminoacyl-tRNA Deacylase. PLoS Biol. 2016 May 25;14(5):e1002465. doi: 10.1371/journal.pbio.1002465., eCollection 2016 May. PMID:27224426 doi:https://dx.doi.org/10.1371/journal.pbio.1002465
↑ Pawar KI, Suma K, Seenivasan A, Kuncha SK, Routh SB, Kruparani SP, Sankaranarayanan R. Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS. Elife. 2017 Mar 31;6:e24001. doi: 10.7554/eLife.24001. PMID:28362257 doi:https://dx.doi.org/10.7554/eLife.24001

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Bhatt TK, Yogavel M, Wydau S, Berwal R, Sharma A. Ligand-bound structures provide atomic snapshots for the catalytic mechanism of D-amino acid deacylase. J Biol Chem. 2010 Feb 19;285(8):5917-30. Epub 2009 Dec 9. PMID:20007323 doi:10.1074/jbc.M109.038562

[2] Ahmad S, Routh SB, Kamarthapu V, Chalissery J, Muthukumar S, Hussain T, Kruparani SP, Deshmukh MV, Sankaranarayanan R. Mechanism of chiral proofreading during translation of the genetic code. Elife. 2013 Dec 3;2(0):e01519. doi: 10.7554/eLife.01519. PMID:24302572 doi:https://dx.doi.org/10.7554/eLife.01519

[3] Routh SB, Pawar KI, Ahmad S, Singh S, Suma K, Kumar M, Kuncha SK, Yadav K, Kruparani SP, Sankaranarayanan R. Elongation Factor Tu Prevents Misediting of Gly-tRNA(Gly) Caused by the Design Behind the Chiral Proofreading Site of D-Aminoacyl-tRNA Deacylase. PLoS Biol. 2016 May 25;14(5):e1002465. doi: 10.1371/journal.pbio.1002465., eCollection 2016 May. PMID:27224426 doi:https://dx.doi.org/10.1371/journal.pbio.1002465

[4] Pawar KI, Suma K, Seenivasan A, Kuncha SK, Routh SB, Kruparani SP, Sankaranarayanan R. Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS. Elife. 2017 Mar 31;6:e24001. doi: 10.7554/eLife.24001. PMID:28362257 doi:https://dx.doi.org/10.7554/eLife.24001

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-{{STRUCTURE_3ko7|  PDB=3ko7  |  SCENE=  }}
-===DTD from Plasmodium falciparum in complex with D-Lysine===
-{{ABSTRACT_PUBMED_20007323}}
-==Function==
+==DTD from Plasmodium falciparum in complex with D-Lysine==
-[[http://www.uniprot.org/uniprot/Q8IIS0_PLAF7 Q8IIS0_PLAF7]] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine (By similarity).[RuleBase:RU003470]
+<StructureSection load='3ko7' size='340' side='right'caption='[[3ko7]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[3ko7]] 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=3KO7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KO7 FirstGlance]. <br>
-[[3ko7]] 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=3KO7 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.21&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DLY:D-LYSINE'>DLY</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ko7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ko7 OCA], [https://pdbe.org/3ko7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ko7 RCSB], [https://www.ebi.ac.uk/pdbsum/3ko7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ko7 ProSAT]</span></td></tr>
-<ref group="xtra">PMID:020007323</ref><references group="xtra"/><references/>
+</table>
-[[Category: Plasmodium falciparum]]
+== Function ==
-[[Category: Bhatt, T K.]]
+[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>
-[[Category: Manickam, Y.]]
+== Evolutionary Conservation ==
-[[Category: Sharma, A.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: D-amino acid]]
+Check<jmol>
-[[Category: D-lysine]]
+  <jmolCheckbox>
-[[Category: Deacylase]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ko/3ko7_consurf.spt"</scriptWhenChecked>
-[[Category: Dtd]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: Hydrolase]]
+    <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=3ko7 ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Plasmodium falciparum 3D7]]
+[[Category: Bhatt TK]]
+[[Category: Manickam Y]]
+[[Category: Sharma A]]

3ko7: Difference between revisions

Latest revision as of 08:30, 20 March 2024

DTD from Plasmodium falciparum in complex with D-Lysine

Structural highlights

Function

Evolutionary Conservation

References

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