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| | ==Aspartyl-tRNA synthetase complexed with aspartic acid== | | ==Aspartyl-tRNA synthetase complexed with aspartic acid== |
| - | <StructureSection load='3nel' size='340' side='right' caption='[[3nel]], [[Resolution|resolution]] 1.95Å' scene=''> | + | <StructureSection load='3nel' size='340' side='right'caption='[[3nel]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3nel]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NEL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NEL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3nel]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NEL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</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]] 1.954Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1b8a|1b8a]], [[3nem|3nem]], [[3nen|3nen]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aspS, TK0492 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311400 "Thermococcus kodakaraensis" Atomi et al. 2004])</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=3nel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nel OCA], [https://pdbe.org/3nel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nel RCSB], [https://www.ebi.ac.uk/pdbsum/3nel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nel 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/Aspartate--tRNA_ligase Aspartate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.12 6.1.1.12] </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=3nel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nel OCA], [http://pdbe.org/3nel PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nel RCSB], [http://www.ebi.ac.uk/pdbsum/3nel PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nel ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SYD_THEKO SYD_THEKO] Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). Is specific for tRNA(Asp) since it aspartylates tRNA(Asn) 3 orders of magnitude less efficiently than tRNA(Asp).<ref>PMID:12149259</ref> <ref>PMID:12660169</ref> <ref>PMID:12730374</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ne/3nel_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ne/3nel_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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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: Thermococcus kodakaraensis atomi et al. 2004]] | + | [[Category: Large Structures]] |
| - | [[Category: Aspartate--tRNA ligase]] | + | [[Category: Thermococcus kodakarensis]] |
| - | [[Category: Moras, D]] | + | [[Category: Moras D]] |
| - | [[Category: Moulinier, L]] | + | [[Category: Moulinier L]] |
| - | [[Category: Schmitt, E]] | + | [[Category: Schmitt E]] |
| - | [[Category: Amino acid]]
| + | |
| - | [[Category: Aminoacyl-trna synthetase]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Mg]]
| + | |
| - | [[Category: Rossmann fold ob fold]]
| + | |
| - | [[Category: Trna]]
| + | |
| Structural highlights
Function
SYD_THEKO Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). Is specific for tRNA(Asp) since it aspartylates tRNA(Asn) 3 orders of magnitude less efficiently than tRNA(Asp).[1] [2] [3]
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
The crystal structure of aspartyl-tRNA synthetase (AspRS) from Pyrococcus kodakaraensis was solved at 1.9 A resolution. The sequence and three-dimensional structure of the catalytic domain are highly homologous to those of eukaryotic AspRSs. In contrast, the N-terminal domain, whose function is to bind the tRNA anticodon, is more similar to that of eubacterial enzymes. Its structure explains the unique property of archaeal AspRSs of accommodating both tRNAAsp and tRNAAsn. Soaking the apo-enzyme crystals with ATP and aspartic acid both separately and together allows the adenylate formation to be followed. Due to the asymmetry of the dimeric enzyme in the crystalline state, different steps of the reaction could be visualized within the same crystal. Four different states of the aspartic acid activation reaction could thus be characterized, revealing the functional correlation of the observed conformational changes. The binding of the amino acid substrate induces movement of two invariant loops which secure the position of the peptidyl moiety for adenylate formation. An unambiguous spatial and functional assignment of three magnesium ion cofactors can be made. This study shows the important role of residues present in both archaeal and eukaryotic AspRSs, but absent from the eubacterial enzymes.
Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation.,Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D EMBO J. 1998 Sep 1;17(17):5227-37. PMID:9724658[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tumbula-Hansen D, Feng L, Toogood H, Stetter KO, Söll D. Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms. J Biol Chem. 2002 Oct 4;277(40):37184-90. PMID:12149259 doi:10.1074/jbc.M204767200
- ↑ Charron C, Roy H, Blaise M, Giege R, Kern D. Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. EMBO J. 2003 Apr 1;22(7):1632-43. PMID:12660169 doi:10.1093/emboj/cdg148
- ↑ Feng L, Tumbula-Hansen D, Toogood H, Soll D. Expanding tRNA recognition of a tRNA synthetase by a single amino acid change. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5676-81. PMID:12730374 doi:10.1073/pnas.0631525100
- ↑ Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 1998 Sep 1;17(17):5227-37. PMID:9724658 doi:10.1093/emboj/17.17.5227
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