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2yxl

From Proteopedia

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{{Seed}}
 
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[[Image:2yxl.png|left|200px]]
 
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==Crystal Structure of PH0851==
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The line below this paragraph, containing "STRUCTURE_2yxl", creates the "Structure Box" on the page.
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<StructureSection load='2yxl' size='340' side='right'caption='[[2yxl]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2yxl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YXL FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.55&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>
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{{STRUCTURE_2yxl| PDB=2yxl | SCENE= }}
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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=2yxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yxl OCA], [https://pdbe.org/2yxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yxl RCSB], [https://www.ebi.ac.uk/pdbsum/2yxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yxl ProSAT], [https://www.topsan.org/Proteins/RSGI/2yxl TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/O58581_PYRHO O58581_PYRHO]
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yx/2yxl_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=2yxl ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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One of the modified nucleosides that frequently occurs in rRNAs and tRNAs is 5-methylcytidine (m(5)C). Escherichia coli Fmu/RsmB/RrmB is an S-adenosyl-L-methionine (AdoMet)-dependent methyltransferase that forms m(5)C967 in 16S rRNA. Fmu/RsmB/RrmB homologues exist not only in bacteria but also in archaea and eukarya and constitute a large orthologous group in the RNA:m(5)C methyltransferase family. In the present study, the crystal structure of a homologue of E. coli Fmu/RsmB/RrmB from the archaeon Pyrococcus horikoshii (PH0851) complexed with an AdoMet analogue was determined at 2.55 A resolution. The structure and sequence of the C-terminal catalytic domain are highly conserved compared with those of E. coli Fmu/RsmB/RrmB. In contrast, the sequence of the N-terminal domain is negligibly conserved between the bacterial and archaeal subfamilies. Nevertheless, the N-terminal domains of PH0851 and E. coli Fmu/RsmB/RrmB are both alpha-helical and adopt a similar topology. Next to the AdoMet-binding site, a positively charged cleft is formed between the N- and C-terminal domains. This cleft is conserved in the archaeal PH0851 homologues and seems to be suitable for binding the RNA substrate.
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===Crystal Structure of PH0851===
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Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase.,Hikida Y, Kuratani M, Bessho Y, Sekine SI, Yokoyama S Acta Crystallogr D Biol Crystallogr. 2010 Dec;66(Pt 12):1301-7. Epub 2010, Nov 16. PMID:21123870<ref>PMID:21123870</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<!--
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_21123870}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2yxl" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 21123870 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_21123870}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2YXL is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YXL OCA].
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[[Category: Pyrococcus horikoshii OT3]]
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[[Category: Bessho Y]]
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==Reference==
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[[Category: Hikida Y]]
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<ref group="xtra">PMID:21123870</ref><references group="xtra"/>
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[[Category: Ishii R]]
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[[Category: Pyrococcus horikoshii ot3]]
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[[Category: Kuratani M]]
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[[Category: Bessho, Y.]]
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[[Category: Sekine S]]
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[[Category: Hikida, Y.]]
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[[Category: Yokoyama S]]
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[[Category: Ishii, R.]]
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[[Category: Kuratani, M.]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Sekine, S.]]
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[[Category: Yokoyama, S.]]
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[[Category: Fmu-homolog]]
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[[Category: Methyltransferase]]
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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 Wed Dec 15 08:14:01 2010''
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Current revision

Crystal Structure of PH0851

PDB ID 2yxl

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