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| | <StructureSection load='3rfa' size='340' side='right'caption='[[3rfa]], [[Resolution|resolution]] 2.05Å' scene=''> | | <StructureSection load='3rfa' size='340' side='right'caption='[[3rfa]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3rfa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RFA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3rfa]] 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=3RFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RFA FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.05Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rf9|3rf9]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rlmN, yfgB, b2517, JW2501 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/23S_rRNA_(adenine(2503)-C(2))-methyltransferase 23S rRNA (adenine(2503)-C(2))-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.192 2.1.1.192] </span></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=3rfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfa OCA], [https://pdbe.org/3rfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rfa RCSB], [https://www.ebi.ac.uk/pdbsum/3rfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rfa ProSAT]</span></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=3rfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rfa OCA], [https://pdbe.org/3rfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rfa RCSB], [https://www.ebi.ac.uk/pdbsum/3rfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rfa ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RLMN_ECOLI RLMN_ECOLI]] Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity. Unmodified tRNA is not a suitable substrate for RlmN, which suggests that RlmN works in a late step during tRNA maturation.<ref>PMID:18025251</ref> <ref>PMID:21415317</ref> <ref>PMID:22891362</ref>
| + | [https://www.uniprot.org/uniprot/RLMN_ECOLI RLMN_ECOLI] Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity. Unmodified tRNA is not a suitable substrate for RlmN, which suggests that RlmN works in a late step during tRNA maturation.<ref>PMID:18025251</ref> <ref>PMID:21415317</ref> <ref>PMID:22891362</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Boal, A K]] | + | [[Category: Boal AK]] |
| - | [[Category: Booker, S J]] | + | [[Category: Booker SJ]] |
| - | [[Category: Grove, T L]] | + | [[Category: Grove TL]] |
| - | [[Category: McLaughlin, M I]] | + | [[Category: McLaughlin MI]] |
| - | [[Category: Rosenzweig, A C]] | + | [[Category: Rosenzweig AC]] |
| - | [[Category: Yennawar, N]] | + | [[Category: Yennawar N]] |
| - | [[Category: Iron sulfur cluster]]
| + | |
| - | [[Category: Methyltransferase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Radical sam]]
| + | |
| - | [[Category: S-adenosylmethionine]]
| + | |
| Structural highlights
Function
RLMN_ECOLI Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity. Unmodified tRNA is not a suitable substrate for RlmN, which suggests that RlmN works in a late step during tRNA maturation.[1] [2] [3]
Publication Abstract from PubMed
The radical SAM (RS) enzymes RlmN and Cfr methylate 23S ribosomal RNA, modifying the C2 or C8 position of adenosine 2503. The methyl groups are installed by a two-step sequence involving initial methylation of a conserved Cys residue (RlmN Cys 355) by SAM. Methyl transfer to the substrate requires reductive cleavage of a second equivalent of SAM. Crystal structures of RlmN and RlmN with SAM show that a single molecule of SAM coordinates the [4Fe-4S] cluster. Residue Cys 355 is S-methylated and located proximal to the SAM methyl group, suggesting that SAM involved in the initial methyl transfer binds at the same site. Thus, RlmN accomplishes its complex reaction with structural economy, harnessing the two most important reactivities of SAM within a single site.
Structural Basis for Methyl Transfer by a Radical SAM Enzyme.,Boal AK, Grove TL, McLaughlin MI, Yennawar NH, Booker SJ, Rosenzweig AC Science. 2011 Apr 28. PMID:21527678[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Toh SM, Xiong L, Bae T, Mankin AS. The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA. 2008 Jan;14(1):98-106. Epub 2007 Nov 19. PMID:18025251 doi:http://dx.doi.org/rna.814408
- ↑ Grove TL, Benner JS, Radle MI, Ahlum JH, Landgraf BJ, Krebs C, Booker SJ. A radically different mechanism for S-adenosylmethionine-dependent methyltransferases. Science. 2011 Apr 29;332(6029):604-7. doi: 10.1126/science.1200877. Epub 2011 Mar, 17. PMID:21415317 doi:http://dx.doi.org/10.1126/science.1200877
- ↑ Benitez-Paez A, Villarroya M, Armengod ME. The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. RNA. 2012 Oct;18(10):1783-95. doi: 10.1261/rna.033266.112. Epub 2012 Aug 13. PMID:22891362 doi:http://dx.doi.org/10.1261/rna.033266.112
- ↑ Boal AK, Grove TL, McLaughlin MI, Yennawar NH, Booker SJ, Rosenzweig AC. Structural Basis for Methyl Transfer by a Radical SAM Enzyme. Science. 2011 Apr 28. PMID:21527678 doi:10.1126/science.1205358
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