3v97: Difference between revisions

Latest revision as of 12:17, 8 November 2023

Crystal structure of bifunctional methyltransferase YcbY (RlmLK) from Escherichia coli, SAH binding

Structural highlights

3v97 is a 2 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 2.2Å
Ligands:	GLC, GOL, PRD_900045, SAH, TRV
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RLMKL_ECOLI Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA. Methylation occurs before assembly of 23S rRNA into 50S subunits.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445 modification, while the C-terminal region of YcbY is responsible for the m(7)G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.

Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA.,Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD Nucleic Acids Res. 2012 Jun;40(11):5138-48. doi: 10.1093/nar/gks160. Epub 2012, Feb 22. PMID:22362734^[4]

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

References

↑ Lesnyak DV, Sergiev PV, Bogdanov AA, Dontsova OA. Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. J Mol Biol. 2006 Nov 17;364(1):20-5. Epub 2006 Sep 8. PMID:17010378 doi:S0022-2836(06)01182-X
↑ Kimura S, Ikeuchi Y, Kitahara K, Sakaguchi Y, Suzuki T, Suzuki T. Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity. Nucleic Acids Res. 2012 May;40(9):4071-85. doi: 10.1093/nar/gkr1287. Epub 2011, Dec 30. PMID:22210896 doi:10.1093/nar/gkr1287
↑ Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD. Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Nucleic Acids Res. 2012 Jun;40(11):5138-48. doi: 10.1093/nar/gks160. Epub 2012, Feb 22. PMID:22362734 doi:10.1093/nar/gks160
↑ Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD. Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Nucleic Acids Res. 2012 Jun;40(11):5138-48. doi: 10.1093/nar/gks160. Epub 2012, Feb 22. PMID:22362734 doi:10.1093/nar/gks160

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Lesnyak DV, Sergiev PV, Bogdanov AA, Dontsova OA. Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. J Mol Biol. 2006 Nov 17;364(1):20-5. Epub 2006 Sep 8. PMID:17010378 doi:S0022-2836(06)01182-X

[2] Kimura S, Ikeuchi Y, Kitahara K, Sakaguchi Y, Suzuki T, Suzuki T. Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity. Nucleic Acids Res. 2012 May;40(9):4071-85. doi: 10.1093/nar/gkr1287. Epub 2011, Dec 30. PMID:22210896 doi:10.1093/nar/gkr1287

[3] Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD. Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Nucleic Acids Res. 2012 Jun;40(11):5138-48. doi: 10.1093/nar/gks160. Epub 2012, Feb 22. PMID:22362734 doi:10.1093/nar/gks160

[4] Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD. Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Nucleic Acids Res. 2012 Jun;40(11):5138-48. doi: 10.1093/nar/gks160. Epub 2012, Feb 22. PMID:22362734 doi:10.1093/nar/gks160

[1]

[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='3v97' size='340' side='right'caption='[[3v97]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3v97]] 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=3V97 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V97 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3v97]] 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=3V97 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V97 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.2&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRV:'>TRV</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900045:octanoyl-sucrose,+esterificated+at+fructose+C6'>PRD_900045</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=TRV:6-O-octanoyl-beta-D-fructofuranose'>TRV</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;'>[[3v8v|3v8v]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rlmL ([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_(guanine(2445)-N(2))-methyltransferase 23S rRNA (guanine(2445)-N(2))-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.173 2.1.1.173] </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=3v97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v97 OCA], [https://pdbe.org/3v97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v97 RCSB], [https://www.ebi.ac.uk/pdbsum/3v97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v97 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RLMKL_ECOLI RLMKL_ECOLI]] Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA. Methylation occurs before assembly of 23S rRNA into 50S subunits.<ref>PMID:17010378</ref> <ref>PMID:22210896</ref> <ref>PMID:22362734</ref>
+[https://www.uniprot.org/uniprot/RLMKL_ECOLI RLMKL_ECOLI] Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA. Methylation occurs before assembly of 23S rRNA into 50S subunits.<ref>PMID:17010378</ref> <ref>PMID:22210896</ref> <ref>PMID:22362734</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Su, X D]]
+[[Category: Su XD]]
-[[Category: Wang, K T]]
+[[Category: Wang KT]]
-[[Category: Ribosome rna]]
-[[Category: Rlmkl]]
-[[Category: Rlml]]
-[[Category: Rna methyltransferase]]
-[[Category: Sah]]
-[[Category: Transferase]]
-[[Category: Ycby]]

3v97: Difference between revisions

Latest revision as of 12:17, 8 November 2023

Crystal structure of bifunctional methyltransferase YcbY (RlmLK) from Escherichia coli, SAH binding

Structural highlights

Function

Publication Abstract from PubMed

References

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