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1qyr

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[[Image:1qyr.jpg|left|200px]]<br /><applet load="1qyr" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1qyr, resolution 2.10&Aring;" />
 
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'''2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase'''<br />
 
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==Overview==
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==2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase==
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The bacterial enzyme KsgA catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaebacteria, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In yeast, and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. Another ortholog has been discovered recently, h-mtTFB in human mitochondria, which has a second function; this enzyme is a nuclear-encoded mitochondrial transcription factor. The KsgA enzymes are homologous to another family of RNA methyltransferases, the Erm enzymes, which methylate a single adenosine base in 23S rRNA and confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. We have crystallized KsgA from Escherichia coli and solved its structure to a resolution of 2.1A. The structure bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to sc-mtTFB, the Saccharomyces cerevisiae version of h-mtTFB. Comparison of the three crystal structures and further study of the KsgA protein will provide insight into this interesting group of enzymes.
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<StructureSection load='1qyr' size='340' side='right'caption='[[1qyr]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QYR FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyr OCA], [https://pdbe.org/1qyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qyr RCSB], [https://www.ebi.ac.uk/pdbsum/1qyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qyr ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qy/1qyr_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1qyr ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1QYR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QYR OCA].
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*[[Adenosine dimethyltransferase 3D structures|Adenosine dimethyltransferase 3D structures]]
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== References ==
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==Reference==
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<references/>
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Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli., O'Farrell HC, Scarsdale JN, Rife JP, J Mol Biol. 2004 May 28;339(2):337-53. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15136037 15136037]
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Farrell, H C.O.]]
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[[Category: O'Farrell HC]]
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[[Category: Rife, J P.]]
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[[Category: Rife JP]]
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[[Category: Scarsdale, J N.]]
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[[Category: Scarsdale JN]]
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[[Category: Wright, H T.]]
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[[Category: Wright HT]]
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[[Category: kasugamycin resistance; adenosine dimethyltransferase; rrna modification]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:45:10 2008''
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Current revision

2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase

PDB ID 1qyr

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