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| | <StructureSection load='6lya' size='340' side='right'caption='[[6lya]], [[Resolution|resolution]] 1.59Å' scene=''> | | <StructureSection load='6lya' size='340' side='right'caption='[[6lya]], [[Resolution|resolution]] 1.59Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6lya]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43340_[[methanococcus_frisius_blotevogel_et_al._1986]] Atcc 43340 [[methanococcus frisius blotevogel et al. 1986]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LYA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LYA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6lya]] 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=6LYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LYA FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EXL:(2S)-2-azanyl-3-(1-methylindol-3-yl)propanoic+acid'>EXL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EXL:1-Methyl-L-tryptophan'>EXL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pylS, DU43_20175, DU67_18120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 ATCC 43340 [[Methanococcus frisius Blotevogel et al. 1986]]])</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=6lya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lya OCA], [https://pdbe.org/6lya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lya RCSB], [https://www.ebi.ac.uk/pdbsum/6lya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lya 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/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>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6lya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lya OCA], [http://pdbe.org/6lya PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lya RCSB], [http://www.ebi.ac.uk/pdbsum/6lya PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lya ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A0F8JXW8_METMZ A0A0F8JXW8_METMZ]] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG.[HAMAP-Rule:MF_01573] | + | [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). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6lya" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6lya" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Tsai, M D]] | + | [[Category: Methanosarcina mazei]] |
| - | [[Category: Wang, Y S]] | + | [[Category: Tsai MD]] |
| - | [[Category: Weng, J H]] | + | [[Category: Wang YS]] |
| - | [[Category: Ligase]] | + | [[Category: Weng JH]] |
| - | [[Category: Trna synthetase]]
| + | |
| 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).
Publication Abstract from PubMed
Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA have been evolved to generate genetically encoded noncanonical amino acids (ncAAs). Use of tryptophan (Trp) analogues with pyrrole ring modification for their spatial and polarity tuning in enzyme activity and substrate specificity is still limited. Herein, we report the application of an evolved PylRS, FOWRS2, for efficient incorporation of five Trp analogues into the deubiquitinase USP30 to decipher the role of W475 for diubiquitin selectivity. Structures of the five FOWRS-C/Trp analogue complexes at 1.7-2.5 A resolution showed multiple ncAA binding modes. The W475 near the USP30 active site was replaced with Trp analogues, and the effect on the activity as well as the selectivity toward diubiquitin linkage types was examined. It was found that the Trp analogue with a formyl group attached to the nitrogen atom of the indole ring led to an improved activity of USP30 likely due to enhanced polar interactions and that another Trp analogue, 3-benzothienyl-l-alanine, induced a unique K6-specificity. Collectively, genetically encoded noncanonical Trp analogues by evolved PylRS.tRNACUA(Pyl) pair unravel the spatial role of USP30-W475 in its diubiquitin selectivity.
Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues.,Jiang HK, Wang YH, Weng JH, Kurkute P, Li CL, Lee MN, Chen PJ, Tseng HW, Tsai MD, Wang YS Biochemistry. 2020 Jun 23;59(24):2205-2209. doi: 10.1021/acs.biochem.0c00307., Epub 2020 Jun 8. PMID:32484330[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Jiang HK, Wang YH, Weng JH, Kurkute P, Li CL, Lee MN, Chen PJ, Tseng HW, Tsai MD, Wang YS. Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues. Biochemistry. 2020 Jun 23;59(24):2205-2209. doi: 10.1021/acs.biochem.0c00307., Epub 2020 Jun 8. PMID:32484330 doi:http://dx.doi.org/10.1021/acs.biochem.0c00307
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