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| | ==X-ray structure of RlmN from Escherichia coli== | | ==X-ray structure of RlmN from Escherichia coli== |
| - | <StructureSection load='3rf9' size='340' side='right' caption='[[3rf9]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3rf9' size='340' side='right'caption='[[3rf9]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3rf9]] 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=3RF9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RF9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3rf9]] 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=3RF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RF9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rfa|3rfa]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rfa|3rfa]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rlmN, yfgB, b2517, JW2501 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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'>[http://en.wikipedia.org/wiki/23S_rRNA_(adenine(2503)-C(2))-methyltransferase 23S rRNA (adenine(2503)-C(2))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.192 2.1.1.192] </span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rf9 OCA], [http://pdbe.org/3rf9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rf9 RCSB], [http://www.ebi.ac.uk/pdbsum/3rf9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rf9 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=3rf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rf9 OCA], [https://pdbe.org/3rf9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rf9 RCSB], [https://www.ebi.ac.uk/pdbsum/3rf9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rf9 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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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| | </StructureSection> | | </StructureSection> |
| | [[Category: Ecoli]] | | [[Category: Ecoli]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Boal, A K]] | | [[Category: Boal, A K]] |
| | [[Category: Booker, S J]] | | [[Category: Booker, S J]] |
| Structural highlights
3rf9 is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , |
| Related: | |
| Gene: | rlmN, yfgB, b2517, JW2501 (ECOLI) |
| Activity: | 23S rRNA (adenine(2503)-C(2))-methyltransferase, with EC number 2.1.1.192 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
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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