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4nbi

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D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 1.86 Angstrom resolution

Structural highlights

4nbi is a 2 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 1.86Å
Ligands:	,
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]

Publication Abstract from PubMed

The biological macromolecular world is homochiral and effective enforcement and perpetuation of this homochirality is essential for cell survival. In this study, we present the mechanistic basis of a configuration-specific enzyme that selectively removes D-amino acids erroneously coupled to tRNAs. The crystal structure of dimeric D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with a substrate-mimicking analog shows how it uses an invariant 'cross-subunit' Gly-cisPro dipeptide to capture the chiral centre of incoming D-aminoacyl-tRNA. While no protein residues are directly involved in catalysis, the unique side chain-independent mode of substrate recognition provides a clear explanation for DTD's ability to act on multiple D-amino acids. The strict chiral specificity elegantly explains how the enriched cellular pool of L-aminoacyl-tRNAs escapes this proofreading step. The study thus provides insights into a fundamental enantioselection process and elucidates a chiral enforcement mechanism with a crucial role in preventing D-amino acid infiltration during the evolution of translational apparatus. DOI: http://dx.doi.org/10.7554/eLife.01519.001.

Mechanism of chiral proofreading during translation of the genetic code.,Ahmad S, Routh SB, Kamarthapu V, Chalissery J, Muthukumar S, Hussain T, Kruparani SP, Deshmukh MV, Sankaranarayanan R Elife. 2013 Dec 3;2(0):e01519. doi: 10.7554/eLife.01519. PMID:24302572^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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:http://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:http://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:http://dx.doi.org/10.7554/eLife.24001
↑ 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:http://dx.doi.org/10.7554/eLife.01519

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4nbi"

@@ Line 1: / Line 1: @@
 ==D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 1.86 Angstrom resolution==
-<StructureSection load='4nbi' size='340' side='right' caption='[[4nbi]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
+<StructureSection load='4nbi' size='340' side='right'caption='[[4nbi]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nbi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Plaf7 Plaf7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NBI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nbi]] is a 2 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=4NBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NBI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D3Y:3-DEOXY-3-(D-TYROSYLAMINO)ADENOSINE'>D3Y</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></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]] 1.86&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nbj|4nbj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D3Y:3-DEOXY-3-(D-TYROSYLAMINO)ADENOSINE'>D3Y</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DTD, PF11_0095 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36329 PLAF7])</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=4nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbi OCA], [https://pdbe.org/4nbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nbi RCSB], [https://www.ebi.ac.uk/pdbsum/4nbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbi ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbi OCA], [http://pdbe.org/4nbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nbi RCSB], [http://www.ebi.ac.uk/pdbsum/4nbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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]
+[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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Plaf7]]
+[[Category: Large Structures]]
-[[Category: Ahmad, S]]
+[[Category: Plasmodium falciparum 3D7]]
-[[Category: Kamarthapu, V]]
+[[Category: Ahmad S]]
-[[Category: Routh, S B]]
+[[Category: Kamarthapu V]]
-[[Category: Sankaranarayanan, R]]
+[[Category: Routh SB]]
-[[Category: Deacylase]]
+[[Category: Sankaranarayanan R]]
-[[Category: Dtd]]
-[[Category: Dtd-like]]
-[[Category: Hydrolase]]

4nbi

From Proteopedia

Current revision

D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 1.86 Angstrom resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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