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| | ==Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylate== | | ==Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylate== |
| - | <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 [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HL2 FirstGlance]. <br> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</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]] 2.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1y2q|1y2q]], [[2hkz|2hkz]], [[2hl0|2hl0]], [[2hl1|2hl1]]</td></tr> | + | <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='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'>[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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hl2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hl2 OCA], [http://pdbe.org/2hl2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hl2 RCSB], [http://www.ebi.ac.uk/pdbsum/2hl2 PDBsum], [http://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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| | ==See Also== | | ==See Also== |
| - | *[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]] | + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrococcus abyssi erauso et al. 1993]] | + | [[Category: Large Structures]] |
| - | [[Category: Threonine--tRNA ligase]] | + | [[Category: Pyrococcus abyssi]] |
| - | [[Category: Hussain, T]] | + | [[Category: Hussain T]] |
| - | [[Category: Kruparani, S P]] | + | [[Category: Kruparani SP]] |
| - | [[Category: Pal, B]] | + | [[Category: Pal B]] |
| - | [[Category: Sankaranarayanan, R]] | + | [[Category: Sankaranarayanan R]] |
| - | [[Category: Aminoacyl-trna synthetase]]
| + | |
| - | [[Category: Editing]]
| + | |
| - | [[Category: Enantioselectivity]]
| + | |
| - | [[Category: Enzyme mechanism]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Translation]]
| + | |
| Structural highlights
Function
SYT_PYRAB
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
To 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 Also
References
- ↑ Hussain T, Kruparani SP, Pal B, Dock-Bregeon AC, Dwivedi S, Shekar MR, Sureshbabu K, Sankaranarayanan R. Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea. EMBO J. 2006 Sep 6;25(17):4152-62. Epub 2006 Aug 10. PMID:16902403
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