2hl2: Difference between revisions
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<StructureSection load='2hl2' size='340' side='right'caption='[[2hl2]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='2hl2' size='340' side='right'caption='[[2hl2]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2hl2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[2hl2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HL2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HL2 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene></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=2hl2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hl2 OCA], [https://pdbe.org/2hl2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hl2 RCSB], [https://www.ebi.ac.uk/pdbsum/2hl2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hl2 ProSAT]</span></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=2hl2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hl2 OCA], [https://pdbe.org/2hl2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hl2 RCSB], [https://www.ebi.ac.uk/pdbsum/2hl2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hl2 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/SYT_PYRAB SYT_PYRAB] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Pyrococcus abyssi]] | ||
[[Category: Hussain | [[Category: Hussain T]] | ||
[[Category: Kruparani | [[Category: Kruparani SP]] | ||
[[Category: Pal | [[Category: Pal B]] | ||
[[Category: Sankaranarayanan | [[Category: Sankaranarayanan R]] | ||
Latest revision as of 11:51, 25 October 2023
Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylateCrystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylate
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedTo ensure a high fidelity during translation, threonyl-tRNA synthetases (ThrRSs) harbor an editing domain that removes noncognate L-serine attached to tRNAThr. Most archaeal ThrRSs possess a unique editing domain structurally similar to D-aminoacyl-tRNA deacylases (DTDs) found in eubacteria and eukaryotes that specifically removes D-amino acids attached to tRNA. Here, we provide mechanistic insights into the removal of noncognate L-serine from tRNAThr by a DTD-like editing module from Pyrococcus abyssi ThrRS (Pab-NTD). High-resolution crystal structures of Pab-NTD with pre- and post-transfer substrate analogs and with L-serine show mutually nonoverlapping binding sites for the seryl moiety. Although the pre-transfer editing is excluded, the analysis reveals the importance of main chain atoms in proper positioning of the post-transfer substrate for its hydrolysis. A single residue has been shown to play a pivotal role in the inversion of enantioselectivity both in Pab-NTD and DTD. The study identifies an enantioselectivity checkpoint that filters opposite chiral molecules and thus provides a fascinating example of how nature has subtly engineered this domain for the selection of chiral molecules during translation. Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea.,Hussain T, Kruparani SP, Pal B, Dock-Bregeon AC, Dwivedi S, Shekar MR, Sureshbabu K, Sankaranarayanan R EMBO J. 2006 Sep 6;25(17):4152-62. Epub 2006 Aug 10. PMID:16902403[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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