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| | <StructureSection load='4pbt' size='340' side='right'caption='[[4pbt]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='4pbt' size='340' side='right'caption='[[4pbt]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4pbt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PBT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4pbt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PBT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2LQ:4-{[(1R,4E)-CYCLOOCT-4-EN-1-YLCARBONYL]AMINO}-L-PHENYLALANINE'>2LQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P4G:1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE'>P4G</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2LQ:4-{[(1R,4E)-CYCLOOCT-4-EN-1-YLCARBONYL]AMINO}-L-PHENYLALANINE'>2LQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P4G:1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE'>P4G</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4pbr|4pbr]], [[4pbs|4pbs]]</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=4pbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pbt OCA], [https://pdbe.org/4pbt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pbt RCSB], [https://www.ebi.ac.uk/pdbsum/4pbt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pbt ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tyrS, MJ0389 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </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=4pbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pbt OCA], [http://pdbe.org/4pbt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pbt RCSB], [http://www.ebi.ac.uk/pdbsum/4pbt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pbt ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SYY_METJA SYY_METJA]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).<ref>PMID:10585437</ref> | + | [https://www.uniprot.org/uniprot/SYY_METJA SYY_METJA] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).<ref>PMID:10585437</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Metja]] | + | [[Category: Methanocaldococcus jannaschii DSM 2661]] |
| - | [[Category: Tyrosine--tRNA ligase]]
| + | [[Category: Cooley RB]] |
| - | [[Category: Cooley, R B]] | + | [[Category: Karplus PA]] |
| - | [[Category: Karplus, P A]] | + | [[Category: Mehl RA]] |
| - | [[Category: Mehl, R A]] | + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Non-natural amino acid]]
| + | |
| - | [[Category: Trna synthetase]]
| + | |
| Structural highlights
Function
SYY_METJA Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).[1]
Publication Abstract from PubMed
The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins is an important tool for understanding biological function. Traditionally, each new ncAA targeted for incorporation requires a resource-consuming process of generating new ncAA aminoacyl tRNA synthetase/tRNACUA pairs. However, the discovery that some tRNA synthetases are "permissive", in that they can incorporate multiple ncAAs, means that it is no longer always necessary to develop a new synthetase for each newly desired ncAA. Developing a better understanding of what factors make ncAA synthetases more permissive would increase the utility of this new approach. Here, we characterized two synthetases selected for the same ncAA that have markedly different "permissivity profiles." Remarkably, the more permissive synthetase incorporated an ncAA for which we had not been able to generate a synthetase through de novo selection methods. Crystal structures revealed that the two synthetases recognize their parent ncAA through a conserved core of interactions, with the more permissive synthetase displaying a greater degree of flexibility in its interaction geometries. We also observed that intraprotein interactions not directly involved in ncAA binding can play a crucial role in synthetase permissivity and suggest that optimization of such interactions might provide an avenue to engineering synthetases with enhanced permissivity.
Gleaning Unexpected Fruits from Hard-Won Synthetases: Probing Principles of Permissivity in Non-canonical Amino Acid-tRNA Synthetases.,Cooley RB, Karplus PA, Mehl RA Chembiochem. 2014 Jul 11. doi: 10.1002/cbic.201402180. PMID:25044993[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Steer BA, Schimmel P. Major anticodon-binding region missing from an archaebacterial tRNA synthetase. J Biol Chem. 1999 Dec 10;274(50):35601-6. PMID:10585437
- ↑ Cooley RB, Karplus PA, Mehl RA. Gleaning Unexpected Fruits from Hard-Won Synthetases: Probing Principles of Permissivity in Non-canonical Amino Acid-tRNA Synthetases. Chembiochem. 2014 Jul 11. doi: 10.1002/cbic.201402180. PMID:25044993 doi:http://dx.doi.org/10.1002/cbic.201402180
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