2yxl: Difference between revisions
From Proteopedia
Jump to navigationJump to search
m Protected "2yxl" [edit=sysop:move=sysop] |
No edit summary |
||
| (6 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Crystal Structure of PH0851== | |||
<StructureSection load='2yxl' size='340' side='right'caption='[[2yxl]], [[Resolution|resolution]] 2.55Å' scene=''> | |||
== Structural highlights == | |||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55Å</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> | |||
<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. | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2yxl" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
== | __TOC__ | ||
< | </StructureSection> | ||
[[Category: Pyrococcus horikoshii]] | [[Category: Large Structures]] | ||
[[Category: Bessho | [[Category: Pyrococcus horikoshii OT3]] | ||
[[Category: Hikida | [[Category: Bessho Y]] | ||
[[Category: Ishii | [[Category: Hikida Y]] | ||
[[Category: Kuratani | [[Category: Ishii R]] | ||
[[Category: Kuratani M]] | |||
[[Category: Sekine | [[Category: Sekine S]] | ||
[[Category: Yokoyama | [[Category: Yokoyama S]] | ||
