5gmc - Revision history

OCA at 11:36, 2 August 2023

2023-08-02T11:36:09Z

←Older revision		Revision as of 11:36, 2 August 2023
Line 1:		Line 1:

	==Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa==		==Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa==
-	<StructureSection load='5gmc' size='340' side='right' caption='[[5gmc]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5gmc' size='340' side='right'caption='[[5gmc]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gmc]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gmc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GMC FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5gm8\|5gm8]], [[5gmb\|5gmb]]</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]] 1.7Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">trmJ ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5gmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmc OCA], [https://pdbe.org/5gmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gmc RCSB], [https://www.ebi.ac.uk/pdbsum/5gmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmc ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(cytidine(32)/uridine(32)-2'-O)-methyltransferase tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.200 2.1.1.200] </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=5gmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmc OCA], [~~http~~://pdbe.org/5gmc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gmc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gmc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmc ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/A0A072ZPM2_PSEAI A0A072ZPM2_PSEAI]] Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA.[RuleBase:RU362024]	+	[https://www.uniprot.org/uniprot/A0A072ZPM2_PSEAI A0A072ZPM2_PSEAI] Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA.[RuleBase:RU362024]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5gmc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gmc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRNA methyltransferase 3D structures\|TRNA methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atichartpongkul, S]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Chionh, Y H]]~~	+
-	~~[[Category: DeMott, M S]]~~	+
-	~~[[Category: Dedon, P C]]~~	+
-	~~[[Category: Fuangthong, M]]~~	+
-	~~[[Category: Jaroensuk, J]]~~	+
-	~~[[Category: Lescar, J]]~~	+
-	~~[[Category: Liew, C W]]~~	+
-	~~[[Category: McBee, M E]]~~	+
-	~~[[Category: Mongkolsuk, S]]~~	+
-	~~[[Category: Prestwich, E G]]~~	+
-	~~[[Category: Thongdee, N]]~~	+
-	~~[[Category: Wong, Y H]]~~	+
-	~~[[Category: Oxidative stress~~]]	+
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Atichartpongkul S]]
-	[[Category: ~~Trmj~~]]	+	[[Category: Chionh YH]]
-	[[Category: ~~Trna methyltransferase~~]]	+	[[Category: DeMott MS]]
-	[[Category: ~~Trna modification~~]]	+	[[Category: Dedon PC]]
-	[[Category: ~~Wobble base~~]]	+	[[Category: Fuangthong M]]
		+	[[Category: Jaroensuk J]]
		+	[[Category: Lescar J]]
		+	[[Category: Liew CW]]
		+	[[Category: McBee ME]]
		+	[[Category: Mongkolsuk S]]
		+	[[Category: Prestwich EG]]
		+	[[Category: Thongdee N]]
		+	[[Category: Wong YH]]

OCA at 07:22, 13 December 2017

2017-12-13T07:22:25Z

←Older revision		Revision as of 07:22, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5gmc' size='340' side='right' caption='[[5gmc]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5gmc' size='340' side='right' caption='[[5gmc]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gmc]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gmc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GMC FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gm8\|5gm8]], [[5gmb\|5gmb]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gm8\|5gm8]], [[5gmb\|5gmb]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trmJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(cytidine(32)/uridine(32)-2'-O)-methyltransferase tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.200 2.1.1.200] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(cytidine(32)/uridine(32)-2'-O)-methyltransferase tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.200 2.1.1.200] </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=5gmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmc OCA], [http://pdbe.org/5gmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gmc RCSB], [http://www.ebi.ac.uk/pdbsum/5gmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmc 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=5gmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmc OCA], [http://pdbe.org/5gmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gmc RCSB], [http://www.ebi.ac.uk/pdbsum/5gmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmc ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/A0A072ZPM2_PSEAI A0A072ZPM2_PSEAI]] Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA.[RuleBase:RU362024]		[[http://www.uniprot.org/uniprot/A0A072ZPM2_PSEAI A0A072ZPM2_PSEAI]] Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA.[RuleBase:RU362024]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteria respond to environmental stresses using a variety of signaling and gene expression pathways, with translational mechanisms being the least well understood. Here, we identified a tRNA methyltransferase in Pseudomonas aeruginosa PA14, trmJ, which confers resistance to oxidative stress. Analysis of tRNA from a trmJ mutant revealed that TrmJ catalyzes formation of Cm, Um, and, unexpectedly, Am. Defined in vitro analyses revealed that tRNA(Met(CAU)) and tRNA(Trp(CCA)) are substrates for Cm formation, tRNA(Gln(UUG)), tRNA(Pro(UGG)), tRNA(Pro(CGG)) and tRNA(His(GUG)) for Um, and tRNA(Pro(GGG)) for Am. tRNA(Ser(UGA)), previously observed as a TrmJ substrate in Escherichia coli, was not modified by PA14 TrmJ. Position 32 was confirmed as the TrmJ target for Am in tRNA(Pro(GGG)) and Um in tRNA(Gln(UUG)) by mass spectrometric analysis. Crystal structures of the free catalytic N-terminal domain of TrmJ show a 2-fold symmetrical dimer with an active site located at the interface between the monomers and a flexible basic loop positioned to bind tRNA, with conformational changes upon binding of the SAM-analog sinefungin. The loss of TrmJ rendered PA14 sensitive to H2O2 exposure, with reduced expression of oxyR-recG, katB-ankB, and katE These results reveal that TrmJ is a tRNA:Cm32/Um32/Am32 methyltransferase involved in translational fidelity and the oxidative stress response.
		+
		+	Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.,Jaroensuk J, Atichartpongkul S, Chionh YH, Wong YH, Liew CW, McBee ME, Thongdee N, Prestwich EG, DeMott MS, Mongkolsuk S, Dedon PC, Lescar J, Fuangthong M Nucleic Acids Res. 2016 Dec 15;44(22):10834-10848. doi: 10.1093/nar/gkw870. Epub , 2016 Sep 28. PMID:27683218<ref>PMID:27683218</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5gmc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:42, 26 October 2016

2016-10-26T18:42:10Z

←Older revision		Revision as of 18:42, 26 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5gmc is ON HOLD~~	+	==Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa==
-		+	<StructureSection load='5gmc' size='340' side='right' caption='[[5gmc]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors: Jaroensuk, J., Atichartpongkul, S., Chionh, Y.H., Wong, Y.H., Liew, C.W., McBee, M.E., Thongdee, N., Prestwich, E.G., DeMott, M.S., Mongkolsuk, S., Dedon, P.C., Lescar, J., Fuangthong, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5gmc]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GMC FirstGlance]. <br>
-	~~Description:~~ Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gm8\|5gm8]], [[5gmb\|5gmb]]</td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(cytidine(32)/uridine(32)-2'-O)-methyltransferase tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.200 2.1.1.200] </span></td></tr>
-	[[~~Category: Mongkolsuk, S~~]]	+	<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=5gmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmc OCA], [http://pdbe.org/5gmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gmc RCSB], [http://www.ebi.ac.uk/pdbsum/5gmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmc ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Liew, C~~.W]]	+	</table>
-	[[~~Category~~: ~~Lescar~~, J]]	+	== Function ==
-	[[~~Category~~: ~~Wong~~, Y.H]]	+	[[http://www.uniprot.org/uniprot/A0A072ZPM2_PSEAI A0A072ZPM2_PSEAI]] Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA.[RuleBase:RU362024]
-	[[~~Category~~: ~~Prestwich~~, E.G]]	+	__TOC__
		+	</StructureSection>
	[[Category: Atichartpongkul, S]]		[[Category: Atichartpongkul, S]]
		+	[[Category: Chionh, Y H]]
		+	[[Category: DeMott, M S]]
		+	[[Category: Dedon, P C]]
	[[Category: Fuangthong, M]]		[[Category: Fuangthong, M]]
-	[[Category: ~~Dedon~~, ~~P.C~~]]	+	[[Category: Jaroensuk, J]]
-	[[Category: ~~Demott~~, ~~M.S~~]]	+	[[Category: Lescar, J]]
-	[[Category: ~~Mcbee~~, M.E]]	+	[[Category: Liew, C W]]
-	[[Category: ~~Chionh~~, ~~Y.H~~]]	+	[[Category: McBee, M E]]
		+	[[Category: Mongkolsuk, S]]
		+	[[Category: Prestwich, E G]]
	[[Category: Thongdee, N]]		[[Category: Thongdee, N]]
-	[[Category: ~~Jaroensuk~~, J]]	+	[[Category: Wong, Y H]]
		+	[[Category: Oxidative stress]]
		+	[[Category: Pseudomonas aeruginosa]]
		+	[[Category: Transferase]]
		+	[[Category: Trmj]]
		+	[[Category: Trna methyltransferase]]
		+	[[Category: Trna modification]]
		+	[[Category: Wobble base]]

OCA at 10:36, 27 July 2016

2016-07-27T10:36:37Z

←Older revision		Revision as of 10:36, 27 July 2016
Line 3:		Line 3:
	The entry 5gmc is ON HOLD		The entry 5gmc is ON HOLD

-	Authors: ~~Juthamas~~ Jaroensuk, ~~Sopapan~~ Atichartpongkul, ~~Yok Hian~~ Chionh, ~~Yee Hwa~~ Wong, ~~Chong Wai~~ Liew, ~~Megan E~~. McBee, ~~Narumon~~ Thongdee, ~~Erin G~~. Prestwich , ~~Michael S~~. DeMott, ~~Skorn~~ Mongkolsuk, ~~Peter C~~. Dedon, ~~Julien~~ Lescar, ~~Mayuree~~ Fuangthong	+	Authors: Jaroensuk, J., Atichartpongkul, S., Chionh, Y.H., Wong, Y.H., Liew, C.W., McBee, M.E., Thongdee, N., Prestwich, E.G., DeMott, M.S., Mongkolsuk, S., Dedon, P.C., Lescar, J., Fuangthong, M.

	Description: Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa		Description: Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Juthamas Jaroensuk~~, ~~Sopapan Atichartpongkul~~, ~~Yok Hian Chionh~~, ~~Yee Hwa~~ Wong, ~~Chong Wai Liew~~, ~~Megan~~ E. ~~Mcbee, Narumon Thongdee, Erin~~ G~~. Prestwich~~ , ~~Michael~~ S. Demott, ~~Skorn Mongkolsuk~~, ~~Peter C~~. ~~Dedon~~, ~~Julien Lescar~~, ~~Mayuree Fuangthong~~]]	+	[[Category: Mongkolsuk, S]]
		+	[[Category: Liew, C.W]]
		+	[[Category: Lescar, J]]
		+	[[Category: Wong, Y.H]]
		+	[[Category: Prestwich, E.G]]
		+	[[Category: Atichartpongkul, S]]
		+	[[Category: Fuangthong, M]]
		+	[[Category: Dedon, P.C]]
		+	[[Category: Demott, M.S]]
		+	[[Category: Mcbee, M.E]]
		+	[[Category: Chionh, Y.H]]
		+	[[Category: Thongdee, N]]
		+	[[Category: Jaroensuk, J]]

OCA: Protected "5gmc" [edit=sysop:move=sysop]

2016-07-26T09:46:28Z

Protected "5gmc" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:46, 26 July 2016

OCA: New page: '''Unreleased structure''' The entry 5gmc is ON HOLD Authors: Juthamas Jaroensuk, Sopapan Atichartpongkul, Yok Hian Chionh, Yee Hwa Wong, Chong Wai Liew, Megan E. McBee, Narumon Thongde...

2016-07-26T09:46:26Z

New page: '''Unreleased structure''' The entry 5gmc is ON HOLD Authors: Juthamas Jaroensuk, Sopapan Atichartpongkul, Yok Hian Chionh, Yee Hwa Wong, Chong Wai Liew, Megan E. McBee, Narumon Thongde...

New page

'''Unreleased structure'''

The entry 5gmc is ON HOLD

Authors: Juthamas Jaroensuk, Sopapan Atichartpongkul, Yok Hian Chionh, Yee Hwa Wong, Chong Wai Liew, Megan E. McBee, Narumon Thongdee, Erin G. Prestwich , Michael S. DeMott, Skorn Mongkolsuk, Peter C. Dedon, Julien Lescar, Mayuree Fuangthong

Description: Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa
[[Category: Unreleased Structures]]
[[Category: Juthamas Jaroensuk, Sopapan Atichartpongkul, Yok Hian Chionh, Yee Hwa Wong, Chong Wai Liew, Megan E. Mcbee, Narumon Thongdee, Erin G. Prestwich , Michael S. Demott, Skorn Mongkolsuk, Peter C. Dedon, Julien Lescar, Mayuree Fuangthong]]