4rrb: Difference between revisions

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 ==N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 2)==
-<StructureSection load='4rrb' size='340' side='right' caption='[[4rrb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='4rrb' size='340' side='right'caption='[[4rrb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rrb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RRB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RRB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rrb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RRB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RRB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rr6|4rr6]], [[4rr7|4rr7]], [[4rr8|4rr8]], [[4rr9|4rr9]], [[4rra|4rra]], [[4rrc|4rrc]], [[4rrd|4rrd]], [[4rrf|4rrf]], [[4rrg|4rrg]], [[4rrh|4rrh]], [[4rri|4rri]], [[4rrj|4rrj]], [[4rrk|4rrk]], [[4rrl|4rrl]], [[4rrm|4rrm]], [[4rrq|4rrq]], [[4rrr|4rrr]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">thrS2, APE_0117.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</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=4rrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rrb OCA], [https://pdbe.org/4rrb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rrb RCSB], [https://www.ebi.ac.uk/pdbsum/4rrb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rrb ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </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=4rrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rrb OCA], [http://pdbe.org/4rrb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rrb RCSB], [http://www.ebi.ac.uk/pdbsum/4rrb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rrb ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/SYTE_AERPE SYTE_AERPE] Freestanding tRNA editing subunit of threonine--tRNA ligase, the catalytic subunit is probably AC Q9YDW0. Deacylates (edits) mischarged L-seryl-tRNA(Thr) in trans; has no activity on correctly charged L-threonyl-tRNA(Thr) (PubMed:26113036). Probably does not aminoacylate tRNA(Thr) (By similarity). Deacylates correctly charged glycyl-tRNA(Gly), but not glycyl-tRNA(Gly)(2'-dA76) (the terminal 2'-OH of tRNA adenine 76 has been dehydroxylated) nor the 2'-fluoro tRNA derivative, strongly suggesting the editing function is catalyzed by the 2'-OH of A76 of tRNA(Thr) (PubMed:26113036).[UniProtKB:Q980D1]<ref>PMID:26113036</ref>
-Proofreading modules of aminoacyl-tRNA synthetases are responsible for enforcing a high fidelity during translation of the genetic code. They use strategically positioned side chains for specifically targeting incorrect aminoacyl-tRNAs. Here, we show that a unique proofreading module possessing a D-aminoacyl-tRNA deacylase fold does not use side chains for imparting specificity or for catalysis, the two hallmark activities of enzymes. We show, using three distinct archaea, that a side-chain-stripped recognition site is fully capable of solving a subtle discrimination problem. While biochemical probing establishes that RNA plays the catalytic role, mechanistic insights from multiple high-resolution snapshots reveal that differential remodelling of the catalytic core at the RNA-peptide interface provides the determinants for correct proofreading activity. The functional crosstalk between RNA and protein elucidated here suggests how primordial enzyme functions could have emerged on RNA-peptide scaffolds before recruitment of specific side chains.
-Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.,Ahmad S, Muthukumar S, Kuncha SK, Routh SB, Yerabham AS, Hussain T, Kamarthapu V, Kruparani SP, Sankaranarayanan R Nat Commun. 2015 Jun 26;6:7552. doi: 10.1038/ncomms8552. PMID:26113036<ref>PMID:26113036</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4rrb" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aerpe]]
+[[Category: Aeropyrum pernix K1]]
-[[Category: Threonine--tRNA ligase]]
+[[Category: Large Structures]]
-[[Category: Ahmad, S]]
+[[Category: Ahmad S]]
-[[Category: Kamarthapu, V]]
+[[Category: Kamarthapu V]]
-[[Category: Muthukumar, S]]
+[[Category: Muthukumar S]]
-[[Category: Sankaranarayanan, R]]
+[[Category: Sankaranarayanan R]]
-[[Category: Yerabham, A S.K]]
+[[Category: Yerabham ASK]]
-[[Category: Dtd-like fold]]
-[[Category: Ligase]]
-[[Category: Proofreading]]