1qyr - Revision history

OCA at 08:18, 14 February 2024

2024-02-14T08:18:54Z

←Older revision		Revision as of 08:18, 14 February 2024
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	<StructureSection load='1qyr' size='340' side='right'caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1qyr' size='340' side='right'caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. 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>	+	<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>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ksgA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895~~])</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]] 2.1Å</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=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>		<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>
	</table>		</table>
	== Function ==		== 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>	+	[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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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].		</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].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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:15136037<ref>PMID:15136037</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1qyr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Farrell, H C.~~O]]	+	[[Category: O'Farrell HC]]
-	[[Category: Rife~~, J P~~]]	+	[[Category: Rife JP]]
-	[[Category: Scarsdale~~, J N~~]]	+	[[Category: Scarsdale JN]]
-	[[Category: Wright~~, H T]]~~	+	[[Category: Wright HT]]
-	~~[[Category: Adenosine dimethyltransferase]]~~	+
-	~~[[Category: Kasugamycin resistance]]~~	+
-	~~[[Category: Rrna modification]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Translation~~]]	+

OCA at 06:03, 28 April 2021

2021-04-28T06:03:29Z

←Older revision		Revision as of 06:03, 28 April 2021
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	<StructureSection load='1qyr' size='340' side='right'caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1qyr' size='340' side='right'caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QYR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyr OCA], [~~http~~://pdbe.org/1qyr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qyr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qyr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qyr ProSAT]</span></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=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>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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>	+	[[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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:00, 24 July 2019

2019-07-24T07:00:38Z

←Older revision		Revision as of 07:00, 24 July 2019
Line 1:		Line 1:

	==2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase==		==2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase==
-	<StructureSection load='1qyr' size='340' side='right' caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1qyr' size='340' side='right'caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYR FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1qyr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qyr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenosine dimethyltransferase 3D structures\|Adenosine dimethyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Farrell, H C.O]]		[[Category: Farrell, H C.O]]
	[[Category: Rife, J P]]		[[Category: Rife, J P]]

OCA at 07:40, 28 February 2018

2018-02-28T07:40:01Z

←Older revision		Revision as of 07:40, 28 February 2018
Line 1:		Line 1:
		+
	==2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase==		==2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase==
	<StructureSection load='1qyr' size='340' side='right' caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1qyr' size='340' side='right' caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYR FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyr OCA], [http://pdbe.org/1qyr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qyr RCSB], [http://www.ebi.ac.uk/pdbsum/1qyr PDBsum]</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=1qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyr OCA], [http://pdbe.org/1qyr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qyr RCSB], [http://www.ebi.ac.uk/pdbsum/1qyr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qyr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qy/1qyr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qy/1qyr_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 1qyr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qyr" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Adenosine dimethyltransferase\|Adenosine dimethyltransferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:21, 7 February 2016

2016-02-07T16:21:07Z

←Older revision		Revision as of 16:21, 7 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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=1qyr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:11, 10 September 2015

2015-09-10T03:11:26Z

←Older revision		Revision as of 03:11, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1qyr' size='340' side='right' caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1qyr' size='340' side='right' caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYR FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qyr RCSB], [http://www.ebi.ac.uk/pdbsum/1qyr PDBsum]</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=1qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyr OCA], [http://pdbe.org/1qyr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qyr RCSB], [http://www.ebi.ac.uk/pdbsum/1qyr PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~KSGA_ECOLI KSGA_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>	+	[[http://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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1qyr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Farrell, H C.O]]		[[Category: Farrell, H C.O]]
	[[Category: Rife, J P]]		[[Category: Rife, J P]]

OCA at 16:39, 24 December 2014

2014-12-24T16:39:11Z

←Older revision		Revision as of 16:39, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qyr RCSB], [http://www.ebi.ac.uk/pdbsum/1qyr PDBsum]</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=1qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qyr RCSB], [http://www.ebi.ac.uk/pdbsum/1qyr PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KSGA_ECOLI KSGA_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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Farrell, H C.O.]]	+	[[Category: Farrell, H C.O]]
-	[[Category: Rife, J P.]]	+	[[Category: Rife, J P]]
-	[[Category: Scarsdale, J N.]]	+	[[Category: Scarsdale, J N]]
-	[[Category: Wright, H T.]]	+	[[Category: Wright, H T]]
	[[Category: Adenosine dimethyltransferase]]		[[Category: Adenosine dimethyltransferase]]
	[[Category: Kasugamycin resistance]]		[[Category: Kasugamycin resistance]]

OCA at 17:18, 29 September 2014

2014-09-29T17:18:48Z

←Older revision		Revision as of 17:18, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1qyr.~~png\|left~~\|200px]]	+	==2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase==
		+	<StructureSection load='1qyr' size='340' side='right' caption='[[1qyr]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qyr]] is a 2 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qyr RCSB], [http://www.ebi.ac.uk/pdbsum/1qyr PDBsum]</span></td></tr>
		+	<table>
		+	== 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/qy/1qyr_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].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~{{STRUCTURE_1qyr\| PDB=1qyr \| SCENE= }}~~	+	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:15136037<ref>PMID:15136037</ref>

-	~~===2~~.~~1 Angstrom Crystal structure~~ of ~~KsgA: A Universally Conserved Adenosine Dimethyltransferase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_15136037}}~~	+	==See Also==
-		+	*[[Adenosine dimethyltransferase\|Adenosine dimethyltransferase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1qyr~~]] is a 2 chain structure with 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].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:015136037<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Farrell, H C.O.]]		[[Category: Farrell, H C.O.]]

OCA: Protected "1qyr" [edit=sysop:move=sysop]

2013-01-02T09:53:18Z

Protected "1qyr" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:53, 2 January 2013

OCA at 09:53, 2 January 2013

2013-01-02T09:53:16Z

←Older revision		Revision as of 09:53, 2 January 2013
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-	{{Seed}}
	[[Image:1qyr.png\|left\|200px]]		[[Image:1qyr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1qyr", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1qyr\| PDB=1qyr \| SCENE= }}		{{STRUCTURE_1qyr\| PDB=1qyr \| SCENE= }}

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

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15136037}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15136037 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15136037}}		{{ABSTRACT_PUBMED_15136037}}

	==About this Structure==		==About this Structure==
-	~~1QYR~~ is a 2 ~~chains~~ structure ~~of sequences~~ 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].	+	[[1qyr]] is a 2 chain structure with 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].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15136037~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015136037</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Farrell, H C.O.]]		[[Category: Farrell, H C.O.]]
Line 32:		Line 20:
	[[Category: Kasugamycin resistance]]		[[Category: Kasugamycin resistance]]
	[[Category: Rrna modification]]		[[Category: Rrna modification]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 15~~:~~04:18 2009''~~	+	[[Category: Translation]]