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2zin

From Proteopedia

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Current revision

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and an ATP analogue

Structural highlights

2zin is a 1 chain structure with sequence from Methanosarcina mazei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.79Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

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

Pyrrolysyl-tRNA synthetase (PylRS) esterifies pyrrolysine to tRNA(Pyl). In this study, N(epsilon)-(tert-butyloxycarbonyl)-L-lysine (BocLys) and N(epsilon)-allyloxycarbonyl-L-lysine (AlocLys) were esterified to tRNA(Pyl) by PylRS. Crystal structures of a PylRS catalytic fragment complexed with BocLys and an ATP analog and with AlocLys-AMP revealed that PylRS requires an N(epsilon)-carbonyl group bearing a substituent with a certain size. A PylRS(Y384F) mutant obtained by random screening exhibited higher in vitro aminoacylation and in vivo amber suppression activities with BocLys, AlocLys, and pyrrolysine than those of the wild-type PylRS. Furthermore, the structure-based Y306A mutation of PylRS drastically increased the in vitro aminoacylation activity for N(epsilon)-benzyloxycarbonyl-L-lysine (ZLys). A PylRS with both the Y306A and Y384F mutations enabled the large-scale preparation (>10 mg per liter medium) of proteins site-specifically containing N(epsilon)-(o-azidobenzyloxycarbonyl)-L-lysine (AzZLys). The AzZLys-containing protein was labeled with a fluorescent probe, by Staudinger ligation.

Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.,Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S Chem Biol. 2008 Nov 24;15(11):1187-97. PMID:19022179^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chem Biol. 2008 Nov 24;15(11):1187-97. PMID:19022179 doi:10.1016/j.chembiol.2008.10.004

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2zin"

Categories: Large Structures | Methanosarcina mazei | Ishii R | Yanagisawa T | Yokoyama S

@@ Line 1: / Line 1: @@
 ==Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and an ATP analogue==
-<StructureSection load='2zin' size='340' side='right' caption='[[2zin]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
+<StructureSection load='2zin' size='340' side='right'caption='[[2zin]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zin]] 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=2ZIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZIN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zin]] 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=2ZIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZIN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LBY:N~6~-(TERT-BUTOXYCARBONYL)-L-LYSINE'>LBY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.79&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2e3c|2e3c]], [[2zcd|2zcd]], [[2zce|2zce]]</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=LBY:N~6~-(TERT-BUTOXYCARBONYL)-L-LYSINE'>LBY</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 ([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=2zin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zin OCA], [https://pdbe.org/2zin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zin RCSB], [https://www.ebi.ac.uk/pdbsum/2zin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zin ProSAT], [https://www.topsan.org/Proteins/RSGI/2zin 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>
-<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=2zin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zin OCA], [http://pdbe.org/2zin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zin RCSB], [http://www.ebi.ac.uk/pdbsum/2zin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zin ProSAT], [http://www.topsan.org/Proteins/RSGI/2zin TOPSAN]</span></td></tr>
 </table>
 == 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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 31: @@
 ==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 ==
@@ Line 39: / Line 37: @@
 __TOC__
 </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: Atp analogue]]
-[[Category: Atp-binding]]
-[[Category: Cytoplasm]]
-[[Category: Ligase]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Non-natural amino acid]]
-[[Category: Nppsfa]]
-[[Category: Nucleotide-binding]]
-[[Category: Protein biosynthesis]]
-[[Category: Pyrrolysine]]
-[[Category: Pyrrolysyl-trna synthetase]]
-[[Category: Rsgi]]
-[[Category: Trna]]
-[[Category: Unnatural amino acid]]

2zin

From Proteopedia

Current revision

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and an ATP analogue

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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