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2yy8

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[[Image:2yy8.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine==
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|PDB= 2yy8 |SIZE=350|CAPTION= <scene name='initialview01'>2yy8</scene>, resolution 2.48&Aring;
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<StructureSection load='2yy8' size='340' side='right'caption='[[2yy8]], [[Resolution|resolution]] 2.48&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Sam+Binding+Site+For+Residue+B+500'>AC1</scene> and <scene name='pdbsite=AC2:Mta+Binding+Site+For+Residue+A+400'>AC2</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MTA:5&#39;-DEOXY-5&#39;-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>
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<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>
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|ACTIVITY=
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</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>
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|GENE=
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<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>
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|DOMAIN=
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<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>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<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://www.ebi.ac.uk/pdbsum/2yy8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2yy8 RCSB]</span>
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== Function ==
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}}
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[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>
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== Evolutionary Conservation ==
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'''Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yy/2yy8_consurf.spt"</scriptWhenChecked>
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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.
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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2YY8 is a [[Single protein]] structure of sequence from [http://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].
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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].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/18068186 18068186]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
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[[Category: Single protein]]
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[[Category: Kuratani M]]
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[[Category: Kuratani, M.]]
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[[Category: Yokoyama S]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Yokoyama, S.]]
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[[Category: deep trefoil knot]]
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[[Category: national project on protein structural and functional analyse]]
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[[Category: nppsfa]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: structural genomic]]
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[[Category: transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:16:35 2008''
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Current revision

Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine

PDB ID 2yy8

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