7o5h

From Proteopedia

(Difference between revisions)

Current revision

Ribosomal methyltransferase KsgA bound to small ribosomal subunit

Structural highlights

7o5h is a 10 chain structure with sequence from Escherichia coli and Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.1Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RSMA_ECOLI Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. Has also a DNA glycosylase/AP lyase activity that removes C mispaired with oxidized T from DNA, and may play a role in protection of DNA against oxidative stress.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Biogenesis of ribosomal subunits involves enzymatic modifications of rRNA that fine-tune functionally important regions. The universally conserved prokaryotic dimethyltransferase KsgA sequentially modifies two universally conserved adenosine residues in helix 45 of the small ribosomal subunit rRNA, which is in proximity of the decoding site. Here we present the cryo-EM structure of Escherichia coli KsgA bound to an E. coli 30S at a resolution of 3.1 A. The high-resolution structure reveals how KsgA recognizes immature rRNA and binds helix 45 in a conformation where one of the substrate nucleotides is flipped-out into the active site. We suggest that successive processing of two adjacent nucleotides involves base-flipping of the rRNA, which allows modification of the second substrate nucleotide without dissociation of the enzyme. Since KsgA is homologous to the essential eukaryotic methyltransferase Dim1 involved in 40S maturation, these results have also implications for understanding eukaryotic ribosome maturation.

Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA.,Stephan NC, Ries AB, Boehringer D, Ban N Nucleic Acids Res. 2021 Jun 21;49(11):6389-6398. doi: 10.1093/nar/gkab430. PMID:34086932^[4]

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

References

↑ van Buul CP, van Knippenberg PH. Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA. Gene. 1985;38(1-3):65-72. PMID:3905517
↑ Zhang-Akiyama QM, Morinaga H, Kikuchi M, Yonekura S, Sugiyama H, Yamamoto K, Yonei S. KsgA, a 16S rRNA adenine methyltransferase, has a novel DNA glycosylase/AP lyase activity to prevent mutations in Escherichia coli. Nucleic Acids Res. 2009 Apr;37(7):2116-25. doi: 10.1093/nar/gkp057. Epub 2009 Feb, 17. PMID:19223326 doi:10.1093/nar/gkp057
↑ Connolly K, Rife JP, Culver G. Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA. Mol Microbiol. 2008 Dec;70(5):1062-75. doi: 10.1111/j.1365-2958.2008.06485.x. PMID:18990185 doi:10.1111/j.1365-2958.2008.06485.x
↑ Stephan NC, Ries AB, Boehringer D, Ban N. Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA. Nucleic Acids Res. 2021 Jun 21;49(11):6389-6398. PMID:34086932 doi:10.1093/nar/gkab430

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7o5h"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7o5h is ON HOLD  until Paper Publication
+==Ribosomal methyltransferase KsgA bound to small ribosomal subunit==
+<StructureSection load='7o5h' size='340' side='right'caption='[[7o5h]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7o5h]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [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=7O5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O5H FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=7o5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o5h OCA], [https://pdbe.org/7o5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o5h RCSB], [https://www.ebi.ac.uk/pdbsum/7o5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o5h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RSMA_ECOLI RSMA_ECOLI] Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. Has also a DNA glycosylase/AP lyase activity that removes C mispaired with oxidized T from DNA, and may play a role in protection of DNA against oxidative stress.<ref>PMID:3905517</ref> <ref>PMID:19223326</ref> <ref>PMID:18990185</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Biogenesis of ribosomal subunits involves enzymatic modifications of rRNA that fine-tune functionally important regions. The universally conserved prokaryotic dimethyltransferase KsgA sequentially modifies two universally conserved adenosine residues in helix 45 of the small ribosomal subunit rRNA, which is in proximity of the decoding site. Here we present the cryo-EM structure of Escherichia coli KsgA bound to an E. coli 30S at a resolution of 3.1 A. The high-resolution structure reveals how KsgA recognizes immature rRNA and binds helix 45 in a conformation where one of the substrate nucleotides is flipped-out into the active site. We suggest that successive processing of two adjacent nucleotides involves base-flipping of the rRNA, which allows modification of the second substrate nucleotide without dissociation of the enzyme. Since KsgA is homologous to the essential eukaryotic methyltransferase Dim1 involved in 40S maturation, these results have also implications for understanding eukaryotic ribosome maturation.
-Authors:
+Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA.,Stephan NC, Ries AB, Boehringer D, Ban N Nucleic Acids Res. 2021 Jun 21;49(11):6389-6398. doi: 10.1093/nar/gkab430. PMID:34086932<ref>PMID:34086932</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7o5h" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Adenosine dimethyltransferase 3D structures|Adenosine dimethyltransferase 3D structures]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Ban N]]
+[[Category: Boehringer D]]
+[[Category: Ries AB]]
+[[Category: Stephan NC]]

7o5h

From Proteopedia

Current revision

Ribosomal methyltransferase KsgA bound to small ribosomal subunit

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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