2frx: Difference between revisions
New page: left|200px<br /><applet load="2frx" size="450" color="white" frame="true" align="right" spinBox="true" caption="2frx, resolution 2.900Å" /> '''Crystal structure o... |
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== | ==Crystal structure of YebU, a m5C RNA methyltransferase from E.coli== | ||
Nucleotide methylations are the most common type of rRNA modification in | <StructureSection load='2frx' size='340' side='right'caption='[[2frx]], [[Resolution|resolution]] 2.90Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2frx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FRX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FRX FirstGlance]. <br> | |||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YebU ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2frx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2frx OCA], [https://pdbe.org/2frx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2frx RCSB], [https://www.ebi.ac.uk/pdbsum/2frx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2frx ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[https://www.uniprot.org/uniprot/RSMF_ECOLI RSMF_ECOLI]] Specifically methylates the cytosine at position 1407 (m5C1407) of 16S rRNA.<ref>PMID:16678201</ref> | |||
== 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/fr/2frx_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=2frx ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Nucleotide methylations are the most common type of rRNA modification in bacteria, and are introduced post-transcriptionally by a wide variety of site-specific enzymes. Three 5-methylcytidine (m(5)C) bases are found in the rRNAs of Escherichia coli and one of these, at nucleotide 1407 in 16 S rRNA, is the modification product of the methyltransferase (MTase) YebU (also called RsmF). YebU requires S-adenosyl-l-methionine (SAM) and methylates C1407 within assembled 30 S subunits, but not in naked 16 S rRNA or within tight-couple 70 S ribosomes. Here, we describe the three-dimensional structure of YebU determined by X-ray crystallography, and we present a molecular model for how YebU specifically recognizes, binds and methylates its ribosomal substrate. The YebU protein has an N-terminal SAM-binding catalytic domain with structural similarity to the equivalent domains in several other m(5)C RNA MTases including RsmB and PH1374. The C-terminal one-third of YebU contains a domain similar to that in pseudouridine synthases and archaeosine-specific transglycosylases (PUA-domain), which was not predicted by sequence alignments. Furthermore, YebU is predicted to contain extended regions of positive electrostatic potential that differ from other RNA-MTase structures, suggesting that YebU interacts with its RNA target in a different manner. Docking of YebU onto the 30 S subunit indicates that the PUA and MTase domains make several contacts with 16 S rRNA as well as with the ribosomal protein S12. The ribosomal protein interactions would explain why the assembled 30 S subunit, and not naked 16 S rRNA, is the preferred substrate for YebU. | |||
The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain.,Hallberg BM, Ericsson UB, Johnson KA, Andersen NM, Douthwaite S, Nordlund P, Beuscher AE 4th, Erlandsen H J Mol Biol. 2006 Jul 21;360(4):774-87. Epub 2006 Jun 6. PMID:16793063<ref>PMID:16793063</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 2frx" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Ericsson, U | <references/> | ||
[[Category: Erlandsen, H | __TOC__ | ||
[[Category: Hallberg, B | </StructureSection> | ||
[[Category: Johnson, K | [[Category: Bacillus coli migula 1895]] | ||
[[Category: Nordlund, P | [[Category: Large Structures]] | ||
[[Category: Ericsson, U B]] | |||
[[Category: | [[Category: Erlandsen, H]] | ||
[[Category: Hallberg, B M]] | |||
[[Category: Johnson, K A]] | |||
[[Category: Nordlund, P]] | |||
[[Category: Rossmann-type s-adenosylmethionine-dependent methyltransferase domain]] | |||
[[Category: Transferase]] | |||
