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| | ==Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase== | | ==Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase== |
| - | <StructureSection load='1uwv' size='340' side='right' caption='[[1uwv]], [[Resolution|resolution]] 1.95Å' scene=''> | + | <StructureSection load='1uwv' size='340' side='right'caption='[[1uwv]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1uwv]] is a 1 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=1UWV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UWV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1uwv]] is a 1 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=1UWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UWV 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>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.95Å</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='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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=1uwv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uwv OCA], [http://pdbe.org/1uwv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uwv RCSB], [http://www.ebi.ac.uk/pdbsum/1uwv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1uwv 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=1uwv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uwv OCA], [https://pdbe.org/1uwv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uwv RCSB], [https://www.ebi.ac.uk/pdbsum/1uwv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uwv ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RLMD_ECOLI RLMD_ECOLI]] Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA.[HAMAP-Rule:MF_01010]<ref>PMID:11779873</ref> <ref>PMID:12907714</ref> | + | [https://www.uniprot.org/uniprot/RLMD_ECOLI RLMD_ECOLI] Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA.[HAMAP-Rule:MF_01010]<ref>PMID:11779873</ref> <ref>PMID:12907714</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Agarwalla, S]]
| + | [[Category: Large Structures]] |
| - | [[Category: Lee, T T]]
| + | [[Category: Agarwalla S]] |
| - | [[Category: Stroud, R M]]
| + | [[Category: Lee TT]] |
| - | [[Category: Iron-sulfur cluster]]
| + | [[Category: Stroud RM]] |
| - | [[Category: Methyltransferase]] | + | |
| - | [[Category: Rna modification]] | + | |
| - | [[Category: Rna processing]] | + | |
| - | [[Category: Transferase]] | + | |
| Structural highlights
1uwv is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.95Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
RLMD_ECOLI Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA.[HAMAP-Rule:MF_01010][1] [2]
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
RumA catalyzes transfer of a methyl group from S-adenosylmethionine (SAM) specifically to uridine 1939 of 23S ribosomal RNA in Escherichia coli to yield 5-methyluridine. We determined the crystal structure of RumA at 1.95 A resolution. The protein is organized into three structural domains: The N-terminal domain contains sequence homology to the conserved TRAM motif and displays a five-stranded beta barrel architecture characteristic of an oligosaccharide/oligonucleotide binding fold. The central domain contains a [Fe(4)S(4)] cluster coordinated by four conserved cysteine residues. The C-terminal domain displays the typical SAM-dependent methyltransferase fold. The catalytic nucleophile Cys389 lies in a motif different from that in DNA 5-methylcytosine methyltransferases. The electrostatic potential surface reveals a predominately positively charged area that covers the concave surface of the first two domains and suggests an RNA binding mode. The iron-sulfur cluster may be involved in the correct folding of the protein or may have a role in RNA binding.
Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase.,Lee TT, Agarwalla S, Stroud RM Structure. 2004 Mar;12(3):397-407. PMID:15016356[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Agarwalla S, Kealey JT, Santi DV, Stroud RM. Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli. J Biol Chem. 2002 Mar 15;277(11):8835-40. Epub 2002 Jan 4. PMID:11779873 doi:10.1074/jbc.M111825200
- ↑ Madsen CT, Mengel-Jorgensen J, Kirpekar F, Douthwaite S. Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 2003 Aug 15;31(16):4738-46. PMID:12907714
- ↑ Lee TT, Agarwalla S, Stroud RM. Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase. Structure. 2004 Mar;12(3):397-407. PMID:15016356 doi:10.1016/j.str.2004.02.009
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