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| | <StructureSection load='3w3s' size='340' side='right'caption='[[3w3s]], [[Resolution|resolution]] 3.10Å' scene=''> | | <StructureSection load='3w3s' size='340' side='right'caption='[[3w3s]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3w3s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Metka Metka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W3S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W3S FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3w3s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5] and [https://en.wikipedia.org/wiki/Methanopyrus_kandleri_AV19 Methanopyrus kandleri AV19]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W3S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W3S FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.095Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">serS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190192 METKA])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </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=3w3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w3s OCA], [https://pdbe.org/3w3s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w3s RCSB], [https://www.ebi.ac.uk/pdbsum/3w3s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w3s 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=3w3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w3s OCA], [https://pdbe.org/3w3s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w3s RCSB], [https://www.ebi.ac.uk/pdbsum/3w3s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w3s ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/SYS2_METKA SYS2_METKA]] Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec) (By similarity).
| + | [https://www.uniprot.org/uniprot/SYS2_METKA SYS2_METKA] Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec) (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Aquifex aeolicus VF5]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Metka]] | + | [[Category: Methanopyrus kandleri AV19]] |
| - | [[Category: Serine--tRNA ligase]]
| + | [[Category: Itoh Y]] |
| - | [[Category: Itoh, Y]] | + | [[Category: Sekine S]] |
| - | [[Category: Sekine, S]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Yokoyama, S]] | + | |
| - | [[Category: Aminoacylation]]
| + | |
| - | [[Category: Class 2 aminoacyl-trna synthetase]]
| + | |
| - | [[Category: Ligase-rna complex]]
| + | |
| - | [[Category: Selenium metabolism]]
| + | |
| - | [[Category: Selenocysteine incorporation]]
| + | |
| - | [[Category: Transfer rna]]
| + | |
| Structural highlights
3w3s is a 2 chain structure with sequence from Aquifex aeolicus VF5 and Methanopyrus kandleri AV19. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 3.095Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
SYS2_METKA Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec) (By similarity).
Publication Abstract from PubMed
Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNASec) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 A crystal structure of the tRNASec from the bacterium Aquifex aeolicus, in complex with the heterologous SerRS from the archaeon Methanopyrus kandleri. The bacterial tRNASec assumes the L-shaped structure, from which the long extra arm protrudes. Although the D-arm conformation and the extra-arm orientation are similar to those of eukaryal/archaeal tRNASecs, A. aeolicus tRNASec has unique base triples, G14:C21:U8 and C15:G20a:G48, which occupy the positions corresponding to the U8:A14 and R15:Y48 tertiary base pairs of canonical tRNAs. Methanopyrus kandleri SerRS exhibited serine ligation activity toward A. aeolicus tRNASec in vitro. The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNASec. Similar interactions exist in the reported tRNASer and SerRS complex structure from the bacterium Thermus thermophilus. Although the catalytic C-terminal domain of M. kandleri SerRS lacks interactions with A. aeolicus tRNASec in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNASec to enter the SerRS catalytic site.
Tertiary structure of bacterial selenocysteine tRNA.,Itoh Y, Sekine SI, Suetsugu S, Yokoyama S Nucleic Acids Res. 2013 May 6. PMID:23649835[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Itoh Y, Sekine SI, Suetsugu S, Yokoyama S. Tertiary structure of bacterial selenocysteine tRNA. Nucleic Acids Res. 2013 May 6. PMID:23649835 doi:10.1093/nar/gkt321
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