2yy8: Difference between revisions

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 ==Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine==
-<StructureSection load='2yy8' size='340' side='right' caption='[[2yy8]], [[Resolution|resolution]] 2.48&Aring;' scene=''>
+<StructureSection load='2yy8' size='340' side='right'caption='[[2yy8]], [[Resolution|resolution]] 2.48&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yy8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YY8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yy8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YY8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 2.48&#8491;</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=2yy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yy8 OCA], [http://pdbe.org/2yy8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yy8 RCSB], [http://www.ebi.ac.uk/pdbsum/2yy8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yy8 ProSAT], [http://www.topsan.org/Proteins/RSGI/2yy8 TOPSAN]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></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=2yy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yy8 OCA], [https://pdbe.org/2yy8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yy8 RCSB], [https://www.ebi.ac.uk/pdbsum/2yy8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yy8 ProSAT], [https://www.topsan.org/Proteins/RSGI/2yy8 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRM56_PYRHO TRM56_PYRHO]] Specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of cytidine at position 56 in tRNAs.<ref>PMID:18068186</ref>
+[https://www.uniprot.org/uniprot/TRM56_PYRHO TRM56_PYRHO] Specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of cytidine at position 56 in tRNAs.<ref>PMID:18068186</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2yy8 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The conserved cytidine residue at position 56 of tRNA contributes to the maintenance of the L-shaped tertiary structure. aTrm56 catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Based on the amino acid sequence, aTrm56 is the most distant member of the SpoU family. Here, we determined the crystal structure of Pyrococcus horikoshii aTrm56 complexed with S-adenosyl-L-methionine at 2.48 A resolution. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot, and a unique C-terminal beta-hairpin. aTrm56 forms a dimer. The S-adenosyl-L-methionine binding and dimerization of aTrm56 were similar to those of the other SpoU members. A structure-based sequence alignment revealed that aTrm56 conserves only motif II, among the four signature motifs. However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate.
-Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA.,Kuratani M, Bessho Y, Nishimoto M, Grosjean H, Yokoyama S J Mol Biol. 2008 Jan 25;375(4):1064-75. Epub 2007 Nov 17. PMID:18068186<ref>PMID:18068186</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2yy8" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus shinkaii]]
+[[Category: Large Structures]]
-[[Category: Kuratani, M]]
+[[Category: Pyrococcus horikoshii]]
-[[Category: Structural genomic]]
+[[Category: Kuratani M]]
-[[Category: Yokoyama, S]]
+[[Category: Yokoyama S]]
-[[Category: Deep trefoil knot]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Rsgi]]
-[[Category: Transferase]]