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| | ==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase== | | ==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase== |
| - | <StructureSection load='2e3c' size='340' side='right' caption='[[2e3c]], [[Resolution|resolution]] 2.65Å' scene=''> | + | <StructureSection load='2e3c' size='340' side='right'caption='[[2e3c]], [[Resolution|resolution]] 2.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_2053 Dsm 2053]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E3C FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2e3c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E3C FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dxg|2dxg]], [[2dxh|2dxh]], [[2dz8|2dz8]]</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]] 2.65Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 DSM 2053])</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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [https://pdbe.org/2e3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [https://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e3c ProSAT], [https://www.topsan.org/Proteins/RSGI/2e3c TOPSAN]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </span></td></tr>
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| - | <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=2e3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e3c OCA], [http://pdbe.org/2e3c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e3c RCSB], [http://www.ebi.ac.uk/pdbsum/2e3c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2e3c ProSAT], [http://www.topsan.org/Proteins/RSGI/2e3c TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA]] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity). | + | [https://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity). |
| | == 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]] |
| - | *[[Pyrrolysyl-tRNA synthetase|Pyrrolysyl-tRNA synthetase]]
| + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Dsm 2053]] | + | [[Category: Large Structures]] |
| - | [[Category: Ishii, R]] | + | [[Category: Methanosarcina mazei]] |
| - | [[Category: Structural genomic]] | + | [[Category: Ishii R]] |
| - | [[Category: Yanagisawa, T]] | + | [[Category: Yanagisawa T]] |
| - | [[Category: Yokoyama, S]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Aminoacyl-trna synthetase]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Pyrrolysine]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Translation]]
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| - | [[Category: Trna]]
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| Structural highlights
Function
PYLS_METMA Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity).
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
Pyrrolysine, a lysine derivative with a bulky pyrroline ring, is the "22nd" genetically encoded amino acid. In the present study, the carboxy-terminal catalytic fragment of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) was analyzed by X-ray crystallography and site-directed mutagenesis. The catalytic fragment ligated tRNA(Pyl) with pyrrolysine nearly as efficiently as the full-length PylRS. We determined the crystal structures of the PylRS catalytic fragment in the substrate-free, ATP analogue (AMPPNP)-bound, and AMPPNP/pyrrolysine-bound forms, and compared them with the previously-reported PylRS structures. The ordering loop and the motif-2 loop undergo conformational changes from the "open" states to the "closed" states upon AMPPNP binding. On the other hand, the beta 7-beta 8 hairpin exhibits multiple conformational states, the open, intermediate (beta 7-open/beta 8-open and beta 7-closed/beta 8-open), and closed states, which are not induced upon substrate binding. The PylRS structures with a docked tRNA suggest that the active-site pocket can accommodate the CCA terminus of tRNA when the motif-2 loop is in the closed state and the beta 7-beta 8 hairpin is in the open or intermediate state. The entrance of the active-site pocket is nearly closed in the closed state of the beta 7-beta 8 hairpin, which may protect the pyrrolysyladenylate intermediate in the absence of tRNA(Pyl). Moreover, a structure-based mutational analysis revealed that hydrophobic residues in the amino acid-binding tunnel are important for accommodating the pyrrolysine side chain and that Asn346 is essential for anchoring the side-chain carbonyl and alpha-amino groups of pyrrolysine. In addition, a docking model of PylRS with tRNA was constructed based on the aspartyl-tRNA synthetase/tRNA structure, and was confirmed by a mutational analysis.
Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase.,Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S J Mol Biol. 2008 May 2;378(3):634-52. Epub 2008 Feb 29. PMID:18387634[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase. J Mol Biol. 2008 May 2;378(3):634-52. Epub 2008 Feb 29. PMID:18387634 doi:10.1016/j.jmb.2008.02.045
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