This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4nbi

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
{{STRUCTURE_4nbi| PDB=4nbi | SCENE= }}
+
==D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 1.86 Angstrom resolution==
-
===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=''>
-
{{ABSTRACT_PUBMED_24302572}}
+
== 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>
 +
</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>
 +
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nbj|4nbj]]</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'>[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://www.rcsb.org/pdb/explore.do?structureId=4nbi RCSB], [http://www.ebi.ac.uk/pdbsum/4nbi PDBsum]</span></td></tr>
 +
</table>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
==Function==
+
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<ref>PMID:24302572</ref>
-
[[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]
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
[[4nbi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBI OCA].
+
</div>
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:024302572</ref><references group="xtra"/><references/>
+
__TOC__
-
[[Category: Ahmad, S.]]
+
</StructureSection>
-
[[Category: Kamarthapu, V.]]
+
[[Category: Plaf7]]
-
[[Category: Routh, S B.]]
+
[[Category: Ahmad, S]]
-
[[Category: Sankaranarayanan, R.]]
+
[[Category: Kamarthapu, V]]
 +
[[Category: Routh, S B]]
 +
[[Category: Sankaranarayanan, R]]
[[Category: Deacylase]]
[[Category: Deacylase]]
[[Category: Dtd]]
[[Category: Dtd]]
[[Category: Dtd-like]]
[[Category: Dtd-like]]
[[Category: Hydrolase]]
[[Category: Hydrolase]]

Revision as of 18:20, 21 December 2014

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

4nbi, resolution 1.86Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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