3fuv: Difference between revisions

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 ==Apo-form of T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in space group P43212==
-<StructureSection load='3fuv' size='340' side='right' caption='[[3fuv]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='3fuv' size='340' side='right'caption='[[3fuv]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3fuv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FUV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3fuv]] is a 3 chain structure with sequence from [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=3FUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FUV FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fut|3fut]], [[3fuu|3fuu]], [[3fuw|3fuw]], [[3fux|3fux]]</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]] 1.95&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ksgA, TTHA0083 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=3fuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fuv OCA], [https://pdbe.org/3fuv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fuv RCSB], [https://www.ebi.ac.uk/pdbsum/3fuv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fuv ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fuv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fuv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fuv RCSB], [http://www.ebi.ac.uk/pdbsum/3fuv PDBsum]</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/3fuv_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fu/3fuv_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3fuv 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Adenosine dimethyltransferase|Adenosine dimethyltransferase]]
+*[[Adenosine dimethyltransferase 3D structures|Adenosine dimethyltransferase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Thermus thermophilus]]
+[[Category: Large Structures]]
-[[Category: Belardinelli, R]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Dahlberg, A E]]
+[[Category: Belardinelli R]]
-[[Category: Demirci, H]]
+[[Category: Dahlberg AE]]
-[[Category: Gregory, S T]]
+[[Category: Demirci H]]
-[[Category: Gualerzi, C]]
+[[Category: Gregory ST]]
-[[Category: Jogl, G]]
+[[Category: Gualerzi C]]
-[[Category: Seri, E]]
+[[Category: Jogl G]]
-[[Category: 16s rrna methyltransferase]]
+[[Category: Seri E]]
-[[Category: Antibiotic resistance]]
-[[Category: Dimethyltransferase]]
-[[Category: Dual-specific methyltransferase]]
-[[Category: Methyltransferase]]
-[[Category: Rna-binding]]
-[[Category: Rrna processing]]
-[[Category: S-adenosyl-l-methionine]]
-[[Category: Transferase]]
-[[Category: Translation]]