4b17: Difference between revisions

Latest revision as of 11:40, 20 December 2023

Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli in complex with S-adenosylmethionine

Structural highlights

4b17 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 2.6Å
Ligands:	CSS, EDO, GOL, SAM, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2]

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Purta E, O'Connor M, Bujnicki JM, Douthwaite S. YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol Microbiol. 2009 Jun;72(5):1147-58. doi: 10.1111/j.1365-2958.2009.06709.x., Epub 2009 Apr 28. PMID:19400805 doi:https://dx.doi.org/10.1111/j.1365-2958.2009.06709.x
↑ Punekar AS, Shepherd TR, Liljeruhm J, Forster AC, Selmer M. Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA. Nucleic Acids Res. 2012 Aug 25. PMID:22923526 doi:https://dx.doi.org/10.1093/nar/gks727
↑ Punekar AS, Shepherd TR, Liljeruhm J, Forster AC, Selmer M. Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA. Nucleic Acids Res. 2012 Aug 25. PMID:22923526 doi:https://dx.doi.org/10.1093/nar/gks727

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OCA

[1] Purta E, O'Connor M, Bujnicki JM, Douthwaite S. YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol Microbiol. 2009 Jun;72(5):1147-58. doi: 10.1111/j.1365-2958.2009.06709.x., Epub 2009 Apr 28. PMID:19400805 doi:https://dx.doi.org/10.1111/j.1365-2958.2009.06709.x

[2] Punekar AS, Shepherd TR, Liljeruhm J, Forster AC, Selmer M. Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA. Nucleic Acids Res. 2012 Aug 25. PMID:22923526 doi:https://dx.doi.org/10.1093/nar/gks727

[3] Punekar AS, Shepherd TR, Liljeruhm J, Forster AC, Selmer M. Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA. Nucleic Acids Res. 2012 Aug 25. PMID:22923526 doi:https://dx.doi.org/10.1093/nar/gks727

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='4b17' size='340' side='right'caption='[[4b17]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4b17]] is a 1 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=4B17 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B17 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4b17]] 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=4B17 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B17 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=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 2.6&#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=SAM:S-ADENOSYLMETHIONINE'>SAM</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;'>[[4atn|4atn]], [[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=4b17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b17 OCA], [https://pdbe.org/4b17 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b17 RCSB], [https://www.ebi.ac.uk/pdbsum/4b17 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b17 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 ==
@@ Line 25: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[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]]

4b17: Difference between revisions

Latest revision as of 11:40, 20 December 2023

Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli in complex with S-adenosylmethionine

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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