7v2p: Difference between revisions
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The | ==T.thermophilus 30S ribosome with KsgA, class K5== | ||
<StructureSection load='7v2p' size='340' side='right'caption='[[7v2p]], [[Resolution|resolution]] 3.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7v2p]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V2P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V2P 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]] 3.3Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7v2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v2p OCA], [https://pdbe.org/7v2p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v2p RCSB], [https://www.ebi.ac.uk/pdbsum/7v2p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v2p ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Methylation of specific nucleotides is integral for ribosomal biogenesis and also serves as a common mechanism to confer antibiotic resistance by pathogenic bacteria. Here, by determining the high-resolution structure of the 30S-KsgA complex by cryo-electron microscopy, a state was captured, where KsgA juxtaposes between helices h44 and h45 of the 30S ribosome, separating them, thereby enabling remodeling of the surrounded rRNA and allowing the cognate site to enter the methylation pocket. With the structure as a guide, several mutant versions of the ribosomes, where interacting bases in the catalytic helix h45 and surrounding helices h44, h24, and h27, were mutated and evaluated for their methylation efficiency revealing factors that direct the enzyme to its cognate site with high fidelity. The biochemical studies show that the three-dimensional environment of the ribosome enables the interaction of select loop regions in KsgA with the ribosome helices paramount to maintain selectivity. | |||
Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases.,Singh J, Raina R, Vinothkumar KR, Anand R ACS Chem Biol. 2022 Apr 15;17(4):829-839. doi: 10.1021/acschembio.1c00732. Epub , 2022 Mar 22. PMID:35316014<ref>PMID:35316014</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Anand | <div class="pdbe-citations 7v2p" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Adenosine dimethyltransferase 3D structures|Adenosine dimethyltransferase 3D structures]] | ||
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]] | |||
*[[Ribosome 3D structures|Ribosome 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus subtilis subsp. subtilis str. 168]] | |||
[[Category: Large Structures]] | |||
[[Category: Thermus thermophilus HB8]] | |||
[[Category: Anand R]] | |||
[[Category: Raina R]] | |||
[[Category: Singh J]] | |||
[[Category: Vinothkumar KR]] | |||
Latest revision as of 08:15, 12 June 2024
T.thermophilus 30S ribosome with KsgA, class K5T.thermophilus 30S ribosome with KsgA, class K5
Structural highlights
FunctionRS17_THET8 One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] Publication Abstract from PubMedMethylation of specific nucleotides is integral for ribosomal biogenesis and also serves as a common mechanism to confer antibiotic resistance by pathogenic bacteria. Here, by determining the high-resolution structure of the 30S-KsgA complex by cryo-electron microscopy, a state was captured, where KsgA juxtaposes between helices h44 and h45 of the 30S ribosome, separating them, thereby enabling remodeling of the surrounded rRNA and allowing the cognate site to enter the methylation pocket. With the structure as a guide, several mutant versions of the ribosomes, where interacting bases in the catalytic helix h45 and surrounding helices h44, h24, and h27, were mutated and evaluated for their methylation efficiency revealing factors that direct the enzyme to its cognate site with high fidelity. The biochemical studies show that the three-dimensional environment of the ribosome enables the interaction of select loop regions in KsgA with the ribosome helices paramount to maintain selectivity. Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases.,Singh J, Raina R, Vinothkumar KR, Anand R ACS Chem Biol. 2022 Apr 15;17(4):829-839. doi: 10.1021/acschembio.1c00732. Epub , 2022 Mar 22. PMID:35316014[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also
References
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