4atn

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Revision as of 07:16, 1 May 2024

Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli

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 <StructureSection load='4atn' size='340' side='right'caption='[[4atn]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4atn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ATN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ATN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4atn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ATN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ATN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.95&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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;'>[[4auk|4auk]]</div></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_(cytidine(2498)-2'-O)-methyltransferase 23S rRNA (cytidine(2498)-2'-O)-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.186 2.1.1.186] </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=4atn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4atn OCA], [https://pdbe.org/4atn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4atn RCSB], [https://www.ebi.ac.uk/pdbsum/4atn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4atn ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RLMM_ECOLI RLMM_ECOLI]] Catalyzes the 2'-O-methylation at nucleotide C2498 in 23S rRNA. Modifies C2498 in naked 23S rRNA, but not in assembled 50S subunits or ribosomes.<ref>PMID:19400805</ref> <ref>PMID:22923526</ref>
+[https://www.uniprot.org/uniprot/RLMM_ECOLI RLMM_ECOLI] Catalyzes the 2'-O-methylation at nucleotide C2498 in 23S rRNA. Modifies C2498 in naked 23S rRNA, but not in assembled 50S subunits or ribosomes.<ref>PMID:19400805</ref> <ref>PMID:22923526</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-RlmM (YgdE) catalyzes the S-adenosyl methionine (AdoMet)-dependent 2'O methylation of C2498 in 23S ribosomal RNA (rRNA) of Escherichia coli. Previous experiments have shown that RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain. Here, we demonstrate RlmM methyltransferase (MTase) activity on in vitro transcribed 23S rRNA and its domain V. We have solved crystal structures of E. coli RlmM at 1.9 A resolution and of an RlmM-AdoMet complex at 2.6 A resolution. RlmM consists of an N-terminal THUMP domain and a C-terminal catalytic Rossmann-like fold MTase domain in a novel arrangement. The catalytic domain of RlmM is closely related to YiiB, TlyA and fibrillarins, with the second K of the catalytic tetrad KDKE shifted by two residues at the C-terminal end of a beta strand compared with most 2'O MTases. The AdoMet-binding site is open and shallow, suggesting that RNA substrate binding may be required to form a conformation needed for catalysis. A continuous surface of conserved positive charge indicates that RlmM uses one side of the two domains and the inter-domain linker to recognize its RNA substrate.
-Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA.,Punekar AS, Shepherd TR, Liljeruhm J, Forster AC, Selmer M Nucleic Acids Res. 2012 Aug 25. PMID:22923526<ref>PMID:22923526</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4atn" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecobd]]
 [[Category: Large Structures]]
-[[Category: Forster, A C]]
+[[Category: Forster AC]]
-[[Category: Liljeruhm, J]]
+[[Category: Liljeruhm J]]
-[[Category: Punekar, A S]]
+[[Category: Punekar AS]]
-[[Category: Selmer, M]]
+[[Category: Selmer M]]
-[[Category: Shepherd, T R]]
+[[Category: Shepherd TR]]
-[[Category: Transferase]]

4atn

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Revision as of 07:16, 1 May 2024

Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli

Structural highlights

Function

References

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