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| | ==Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group P21212== | | ==Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group P21212== |
| - | <StructureSection load='3m6x' size='340' side='right' caption='[[3m6x]], [[Resolution|resolution]] 1.68Å' scene=''> | + | <StructureSection load='3m6x' size='340' side='right'caption='[[3m6x]], [[Resolution|resolution]] 1.68Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3m6x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M6X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M6X FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3m6x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M6X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M6X FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.676Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2frx|2frx]], [[3m6u|3m6u]], [[3m6v|3m6v]], [[3m6w|3m6w]]</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=3m6x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m6x OCA], [https://pdbe.org/3m6x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m6x RCSB], [https://www.ebi.ac.uk/pdbsum/3m6x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m6x ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA1387 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3m6x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m6x OCA], [http://pdbe.org/3m6x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3m6x RCSB], [http://www.ebi.ac.uk/pdbsum/3m6x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3m6x ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RSMF_THET8 RSMF_THET8] Specifically methylates the cytosines at positions 1400 (m5C1400), 1404 (m5C1404) and 1407 (m5C1407) of 16S rRNA. C1400, C1404 and C1407 are methylated in a 30S subunit substrate, but only C1400 and C1404 are methylated when naked 16S rRNA is the substrate. Methylation by RsmF may facilitate growth at temperatures outside the optimal growth temperature.<ref>PMID:20558545</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m6/3m6x_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m6/3m6x_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Thet8]] | + | [[Category: Large Structures]] |
| - | [[Category: Cadambi, A]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Demirci, H]] | + | [[Category: Cadambi A]] |
| - | [[Category: Gregory, S T]] | + | [[Category: Demirci H]] |
| - | [[Category: Hansen, T]] | + | [[Category: Gregory ST]] |
| - | [[Category: Jogl, G]] | + | [[Category: Hansen T]] |
| - | [[Category: Kirpekar, F]] | + | [[Category: Jogl G]] |
| - | [[Category: Larsen, H G.L]] | + | [[Category: Kirpekar F]] |
| - | [[Category: Rasmussen, A]] | + | [[Category: Larsen HGL]] |
| - | [[Category: 5-methylcytidine]]
| + | [[Category: Rasmussen A]] |
| - | [[Category: Adomet]]
| + | |
| - | [[Category: Methyltransferase]]
| + | |
| - | [[Category: Multi-specific]]
| + | |
| - | [[Category: Rrna methyltransferase]]
| + | |
| - | [[Category: Rsmf]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
RSMF_THET8 Specifically methylates the cytosines at positions 1400 (m5C1400), 1404 (m5C1404) and 1407 (m5C1407) of 16S rRNA. C1400, C1404 and C1407 are methylated in a 30S subunit substrate, but only C1400 and C1404 are methylated when naked 16S rRNA is the substrate. Methylation by RsmF may facilitate growth at temperatures outside the optimal growth temperature.[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
Cells devote a significant effort toward the production of multiple modified nucleotides in rRNAs, which fine tune the ribosome function. Here, we report that two methyltransferases, RsmB and RsmF, are responsible for all four 5-methylcytidine (m(5)C) modifications in 16S rRNA of Thermus thermophilus. Like Escherichia coli RsmB, T. thermophilus RsmB produces m(5)C967. In contrast to E. coli RsmF, which introduces a single m(5)C1407 modification, T. thermophilus RsmF modifies three positions, generating m(5)C1400 and m(5)C1404 in addition to m(5)C1407. These three residues are clustered near the decoding site of the ribosome, but are situated in distinct structural contexts, suggesting a requirement for flexibility in the RsmF active site that is absent from the E. coli enzyme. Two of these residues, C1400 and C1404, are sufficiently buried in the mature ribosome structure so as to require extensive unfolding of the rRNA to be accessible to RsmF. In vitro, T. thermophilus RsmF methylates C1400, C1404, and C1407 in a 30S subunit substrate, but only C1400 and C1404 when naked 16S rRNA is the substrate. The multispecificity of T. thermophilus RsmF is potentially explained by three crystal structures of the enzyme in a complex with cofactor S-adenosyl-methionine at up to 1.3 A resolution. In addition to confirming the overall structural similarity to E. coli RsmF, these structures also reveal that key segments in the active site are likely to be dynamic in solution, thereby expanding substrate recognition by T. thermophilus RsmF.
Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus.,Demirci H, Larsen LH, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G RNA. 2010 Aug;16(8):1584-96. Epub 2010 Jun 17. PMID:20558545[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Demirci H, Larsen LH, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G. Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. RNA. 2010 Aug;16(8):1584-96. Epub 2010 Jun 17. PMID:20558545 doi:10.1261/rna.2088310
- ↑ Demirci H, Larsen LH, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G. Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. RNA. 2010 Aug;16(8):1584-96. Epub 2010 Jun 17. PMID:20558545 doi:10.1261/rna.2088310
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