2yxl: Difference between revisions

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{{Seed}}
[[Image:2yxl.png|left|200px]]


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==Crystal Structure of PH0851==
The line below this paragraph, containing "STRUCTURE_2yxl", creates the "Structure Box" on the page.
<StructureSection load='2yxl' size='340' side='right'caption='[[2yxl]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
-->
<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>
{{STRUCTURE_2yxl|  PDB=2yxl  |  SCENE=  }}
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O58581_PYRHO O58581_PYRHO]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yx/2yxl_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===Crystal Structure of PH0851===
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>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
2YXL 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=2YXL OCA].
<div class="pdbe-citations 2yxl" style="background-color:#fffaf0;"></div>
[[Category: Pyrococcus horikoshii]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Bessho, Y.]]
__TOC__
[[Category: Hikida, Y.]]
</StructureSection>
[[Category: Ishii, R.]]
[[Category: Large Structures]]
[[Category: Kuratani, M.]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Bessho Y]]
[[Category: Sekine, S.]]
[[Category: Hikida Y]]
[[Category: Yokoyama, S.]]
[[Category: Ishii R]]
[[Category: Fmu-homolog]]
[[Category: Kuratani M]]
[[Category: Methyltransferase]]
[[Category: Sekine S]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Yokoyama S]]
[[Category: Nppsfa]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
 
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Retrieved from "https://proteopedia.org/2yxl"