3fux: Difference between revisions
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< | ==T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with 5'-methylthioadenosine in space group P212121== | ||
<StructureSection load='3fux' size='340' side='right'caption='[[3fux]], [[Resolution|resolution]] 1.68Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3fux]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FUX FirstGlance]. <br> | |||
or | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</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;'>[[3fut|3fut]], [[3fuu|3fuu]], [[3fuv|3fuv]], [[3fuw|3fuw]]</div></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ksgA, TTHA0083 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=3fux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fux OCA], [https://pdbe.org/3fux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fux RCSB], [https://www.ebi.ac.uk/pdbsum/3fux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fux ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[https://www.uniprot.org/uniprot/RSMA_THET8 RSMA_THET8]] 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.[HAMAP-Rule:MF_00607] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fu/3fux_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3fux ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Posttranscriptional modification of ribosomal RNA (rRNA) occurs in all kingdoms of life. The S-adenosyl-L-methionine-dependent methyltransferase KsgA introduces the most highly conserved rRNA modification, the dimethylation of A1518 and A1519 of 16S rRNA. Loss of this dimethylation confers resistance to the antibiotic kasugamycin. Here, we report biochemical studies and high-resolution crystal structures of KsgA from Thermus thermophilus. Methylation of 30S ribosomal subunits by T. thermophilus KsgA is more efficient at low concentrations of magnesium ions, suggesting that partially unfolded RNA is the preferred substrate. The overall structure is similar to that of other methyltransferases but contains an additional alpha-helix in a novel N-terminal extension. Comparison of the apoenzyme with complex structures with 5'-methylthioadenosine or adenosine bound in the cofactor-binding site reveals novel features when compared with related enzymes. Several mobile loop regions that restrict access to the cofactor-binding site are observed. In addition, the orientation of residues in the substrate-binding site indicates that conformational changes are required for binding two adjacent residues of the substrate rRNA. | |||
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.,Demirci H, Belardinelli R, Seri E, Gregory ST, Gualerzi C, Dahlberg AE, Jogl G J Mol Biol. 2009 May 1;388(2):271-82. Epub 2009 Mar 12. PMID:19285505<ref>PMID:19285505</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3fux" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Adenosine dimethyltransferase 3D structures|Adenosine dimethyltransferase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Thet8]] | |||
[[Category: Belardinelli, R]] | |||
== | [[Category: Dahlberg, A E]] | ||
< | [[Category: Demirci, H]] | ||
[[Category: | [[Category: Gregory, S T]] | ||
[[Category: Belardinelli, R | [[Category: Gualerzi, C]] | ||
[[Category: Dahlberg, A E | [[Category: Jogl, G]] | ||
[[Category: Demirci, H | [[Category: Seri, E]] | ||
[[Category: Gregory, S T | |||
[[Category: Gualerzi, C | |||
[[Category: Jogl, G | |||
[[Category: Seri, E | |||
[[Category: 16s rrna methyltransferase]] | [[Category: 16s rrna methyltransferase]] | ||
[[Category: Antibiotic resistance]] | [[Category: Antibiotic resistance]] | ||
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[[Category: Transferase]] | [[Category: Transferase]] | ||
[[Category: Translation]] | [[Category: Translation]] | ||
Latest revision as of 11:12, 2 March 2022
T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with 5'-methylthioadenosine in space group P212121T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with 5'-methylthioadenosine in space group P212121
Structural highlights
Function[RSMA_THET8] 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.[HAMAP-Rule:MF_00607] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedPosttranscriptional modification of ribosomal RNA (rRNA) occurs in all kingdoms of life. The S-adenosyl-L-methionine-dependent methyltransferase KsgA introduces the most highly conserved rRNA modification, the dimethylation of A1518 and A1519 of 16S rRNA. Loss of this dimethylation confers resistance to the antibiotic kasugamycin. Here, we report biochemical studies and high-resolution crystal structures of KsgA from Thermus thermophilus. Methylation of 30S ribosomal subunits by T. thermophilus KsgA is more efficient at low concentrations of magnesium ions, suggesting that partially unfolded RNA is the preferred substrate. The overall structure is similar to that of other methyltransferases but contains an additional alpha-helix in a novel N-terminal extension. Comparison of the apoenzyme with complex structures with 5'-methylthioadenosine or adenosine bound in the cofactor-binding site reveals novel features when compared with related enzymes. Several mobile loop regions that restrict access to the cofactor-binding site are observed. In addition, the orientation of residues in the substrate-binding site indicates that conformational changes are required for binding two adjacent residues of the substrate rRNA. Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.,Demirci H, Belardinelli R, Seri E, Gregory ST, Gualerzi C, Dahlberg AE, Jogl G J Mol Biol. 2009 May 1;388(2):271-82. Epub 2009 Mar 12. PMID:19285505[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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