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| | <StructureSection load='3c0k' size='340' side='right'caption='[[3c0k]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='3c0k' size='340' side='right'caption='[[3c0k]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3c0k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C0K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3C0K FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3c0k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C0K 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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3c0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c0k OCA], [http://pdbe.org/3c0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c0k RCSB], [http://www.ebi.ac.uk/pdbsum/3c0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3c0k ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=3c0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c0k OCA], [https://pdbe.org/3c0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c0k RCSB], [https://www.ebi.ac.uk/pdbsum/3c0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c0k ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RLMI_ECOLI RLMI_ECOLI]] Specifically methylates the cytosine at position 1962 (m5C1962) of 23S rRNA. Methylation occurs before assembly of 23S rRNA into 50S subunits.<ref>PMID:18786544</ref> | + | [https://www.uniprot.org/uniprot/RLMI_ECOLI RLMI_ECOLI] Specifically methylates the cytosine at position 1962 (m5C1962) of 23S rRNA. Methylation occurs before assembly of 23S rRNA into 50S subunits.<ref>PMID:18786544</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/3c0k_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/3c0k_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bujnicki, J]] | + | [[Category: Bujnicki J]] |
| - | [[Category: Jayaraman, S]] | + | [[Category: Jayaraman S]] |
| - | [[Category: Subramanian, S]] | + | [[Category: Subramanian S]] |
| - | [[Category: Adomet dependent methyltransferase fold]]
| + | |
| - | [[Category: Pua domain]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
RLMI_ECOLI Specifically methylates the cytosine at position 1962 (m5C1962) of 23S rRNA. Methylation occurs before assembly of 23S rRNA into 50S subunits.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Methylation is the most common RNA modification in the three domains of life. Transfer of the methyl group from S-adenosyl-l-methionine (AdoMet) to specific atoms of RNA nucleotides is catalyzed by methyltransferase (MTase) enzymes. The rRNA MTase RlmI (rRNA large subunit methyltransferase gene I; previously known as YccW) specifically modifies Escherichia coli 23S rRNA at nucleotide C1962 to form 5-methylcytosine. Here, we report the crystal structure of RlmI refined at 2 A to a final R-factor of 0.194 (R(free)=0.242). The RlmI molecule comprises three domains: the N-terminal PUA domain; the central domain, which resembles a domain previously found in RNA:5-methyluridine MTases; and the C-terminal catalytic domain, which contains the AdoMet-binding site. The central and C-terminal domains are linked by a beta-hairpin structure that has previously been observed in several MTases acting on nucleic acids or proteins. Based on bioinformatics analyses, we propose a model for the RlmI-AdoMet-RNA complex. Comparative structural analyses of RlmI and its homologs provide insight into the potential function of several structures that have been solved by structural genomics groups and furthermore indicate that the evolutionary paths of RNA and DNA 5-methyluridine and 5-methylcytosine MTases have been closely intertwined.
Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes.,Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM, Sivaraman J J Mol Biol. 2008 Nov 14;383(3):652-66. Epub 2008 Aug 29. PMID:18789337[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Purta E, O'Connor M, Bujnicki JM, Douthwaite S. YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. J Mol Biol. 2008 Nov 14;383(3):641-51. Epub 2008 Aug 29. PMID:18786544 doi:http://dx.doi.org/S0022-2836(08)01068-1
- ↑ Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM, Sivaraman J. Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J Mol Biol. 2008 Nov 14;383(3):652-66. Epub 2008 Aug 29. PMID:18789337 doi:10.1016/j.jmb.2008.08.062
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