5wt3 - Revision history

OCA at 16:53, 8 November 2023

OCA — Wed, 08 Nov 2023 16:53:34 GMT

←Older revision		Revision as of 16:53, 8 November 2023
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	<StructureSection load='5wt3' size='340' side='right'caption='[[5wt3]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='5wt3' size='340' side='right'caption='[[5wt3]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wt3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrab Pyrab~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WT3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WT3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wt3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WT3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></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]] 3.204Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5wt1\|5wt1~~]]</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>trm5a, PYRAB01130, PAB2272 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=272844 PYRAB])</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=5wt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wt3 OCA], [https://pdbe.org/5wt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wt3 RCSB], [https://www.ebi.ac.uk/pdbsum/5wt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wt3 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_(guanine(37)~~-~~N(1))~~-~~methyltransferase tRNA (guanine(37)~~-~~N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228]~~ </~~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=5wt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wt3 OCA], [~~http~~://pdbe.org/5wt3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wt3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wt3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wt3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~TRM5A_PYRAB TRM5A_PYRAB~~]~~] Specifically methylates~~ the N1 ~~position~~ of guanosine~~-37 in tRNA(Phe). In vitro, can also methylate~~ the C7 ~~position~~ of 4-demethylwyosine (imG-14).<ref>PMID:20382657</ref>	+	[https://www.uniprot.org/uniprot/TAW22_PYRAB TAW22_PYRAB] Catalyzes both the N1-methylation of guanosine and the C7-methylation of 4-demethylwyosine (imG-14) at position 37 in tRNA(Phe).<ref>PMID:20382657</ref> <ref>PMID:27852927</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5wt3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5wt3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRNA methyltransferase 3D structures\|TRNA methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyrab~~]]	+	[[Category: Pyrococcus abyssi GE5]]
-	[[Category: Jia, Q]]	+	[[Category: Jia Q]]
-	[[Category: Wang, C]]	+	[[Category: Wang C]]
-	[[Category: Xie, W]]	+	[[Category: Xie W]]
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Transferase-rna complex]]~~	+
-	~~[[Category: Trm5a]]~~	+
-	~~[[Category: Wyosine hypermodification~~]]	+

OCA at 09:12, 18 December 2019

OCA — Wed, 18 Dec 2019 09:12:38 GMT

←Older revision		Revision as of 09:12, 18 December 2019
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	==Pyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNA==		==Pyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNA==
-	<StructureSection load='5wt3' size='340' side='right' caption='[[5wt3]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='5wt3' size='340' side='right'caption='[[5wt3]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wt3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WT3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WT3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wt3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrab Pyrab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WT3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WT3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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">[[5wt1\|5wt1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wt1\|5wt1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm5a, PYRAB01130, PAB2272 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </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_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </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=5wt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wt3 OCA], [http://pdbe.org/5wt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wt3 RCSB], [http://www.ebi.ac.uk/pdbsum/5wt3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wt3 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=5wt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wt3 OCA], [http://pdbe.org/5wt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wt3 RCSB], [http://www.ebi.ac.uk/pdbsum/5wt3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wt3 ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TRM5A_PYRAB TRM5A_PYRAB]] Specifically methylates the N1 position of guanosine-37 in tRNA(Phe). In vitro, can also methylate the C7 position of 4-demethylwyosine (imG-14).<ref>PMID:20382657</ref>		[[http://www.uniprot.org/uniprot/TRM5A_PYRAB TRM5A_PYRAB]] Specifically methylates the N1 position of guanosine-37 in tRNA(Phe). In vitro, can also methylate the C7 position of 4-demethylwyosine (imG-14).<ref>PMID:20382657</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The wyosine derivatives present at position 37 in transfer RNAs (tRNAs) are critical for reading frame maintenance. The methyltransferase Trm5a from Pyrococcus abyssi (PaTrm5a) plays a key role in this hypermodification process in generating m(1)G37 and imG2, two products of the wyosine biosynthetic pathway, through two methyl transfers to distinct substrates, but the mechanism is currently unknown. We report two cocrystal structures of PaTrm5a in complex with tRNA(Phe) and reveal the structural basis for substrate recognition, which was supported by in vitro activity assays. The crystal structures showed that the D1 domain of the enzyme undergoes large conformational changes upon the binding of tRNA. The deletion of this domain greatly reduces the affinity and activity of PaTrm5a toward its RNA substrate, indicating that the enzyme recognizes the overall shape of tRNA. Using the small-angle x-ray scattering technique and crystallographic analysis, we discovered that PaTrm5a adopts distinct open conformations before and after the binding of tRNA. Last, through structure comparison with its ortholog Methanococcus jannaschii Trm5b (MjTrm5b), we propose a reaction mechanism for the double methylation capability of this unique enzyme.
		+
		+	Structural insight into the methyltransfer mechanism of the bifunctional Trm5.,Wang C, Jia Q, Zeng J, Chen R, Xie W Sci Adv. 2017 Dec 1;3(12):e1700195. doi: 10.1126/sciadv.1700195. eCollection 2017, Dec. PMID:29214216<ref>PMID:29214216</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5wt3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrab]]
	[[Category: Jia, Q]]		[[Category: Jia, Q]]
	[[Category: Wang, C]]		[[Category: Wang, C]]

OCA at 06:59, 13 December 2017

OCA — Wed, 13 Dec 2017 06:59:53 GMT

←Older revision		Revision as of 06:59, 13 December 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5wt3 is ~~ON HOLD~~ ~~until Dec 09 2018~~	+	==Pyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNA==
-		+	<StructureSection load='5wt3' size='340' side='right' caption='[[5wt3]], [[Resolution\|resolution]] 3.20Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5wt3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WT3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WT3 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wt1\|5wt1]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </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=5wt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wt3 OCA], [http://pdbe.org/5wt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wt3 RCSB], [http://www.ebi.ac.uk/pdbsum/5wt3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wt3 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TRM5A_PYRAB TRM5A_PYRAB]] Specifically methylates the N1 position of guanosine-37 in tRNA(Phe). In vitro, can also methylate the C7 position of 4-demethylwyosine (imG-14).<ref>PMID:20382657</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Jia, Q]]
		+	[[Category: Wang, C]]
		+	[[Category: Xie, W]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Transferase-rna complex]]
		+	[[Category: Trm5a]]
		+	[[Category: Wyosine hypermodification]]

OCA at 15:26, 2 January 2017

OCA — Mon, 02 Jan 2017 15:26:50 GMT

←Older revision		Revision as of 15:26, 2 January 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5wt3 is ON HOLD	+	The entry 5wt3 is ON HOLD until Dec 09 2018

	Authors:		Authors:

OCA: Protected "5wt3" [edit=sysop:move=sysop]

OCA — Thu, 22 Dec 2016 20:40:48 GMT

Protected "5wt3" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:40, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5wt3 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 22 Dec 2016 20:40:46 GMT

New page: '''Unreleased structure''' The entry 5wt3 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5wt3 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]