5yac - Revision history

OCA at 08:25, 22 November 2023

2023-11-22T08:25:22Z

←Older revision		Revision as of 08:25, 22 November 2023
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	==Crystal structure of WT Trm5b from Pyrococcus abyssi==		==Crystal structure of WT Trm5b from Pyrococcus abyssi==
-	<StructureSection load='5yac' size='340' side='right' caption='[[5yac]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='5yac' size='340' side='right'caption='[[5yac]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yac]] is a 1 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=5YAC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YAC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yac]] is a 1 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=5YAC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YAC FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>trm5b, PYRAB07390, PAB0505 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=272844 PYRAB])</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]] 3.3Å</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'>[https://proteopedia.org/fgij/fg.htm?mol=5yac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yac OCA], [https://pdbe.org/5yac PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yac RCSB], [https://www.ebi.ac.uk/pdbsum/5yac PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yac 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=5yac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yac OCA], [~~http~~://pdbe.org/5yac PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yac RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yac PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yac ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TRM5B_PYRAB TRM5B_PYRAB]] Specifically methylates the N1 position of guanosine-37 in various tRNAs.<ref>PMID:20382657</ref>	+	[https://www.uniprot.org/uniprot/TRM5B_PYRAB TRM5B_PYRAB] Specifically methylates the N1 position of guanosine-37 in various tRNAs.<ref>PMID:20382657</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[TRNA methyltransferase\|TRNA methyltransferase]]	+	*[[TRNA methyltransferase 3D structures\|TRNA methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrab~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Wu, J~~]]	+	[[Category: Pyrococcus abyssi GE5]]
-	[[Category: ~~Xie, W~~]]	+	[[Category: Wu J]]
-	[[Category: ~~Open conformation]]~~	+	[[Category: Xie W]]
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Trna maturation]]~~	+
-	~~[[Category: Trna methyltransferase]]~~	+
-	~~[[Category: Wyosine biosynthesis~~]]	+

OCA at 09:35, 18 July 2018

2018-07-18T09:35:48Z

←Older revision		Revision as of 09:35, 18 July 2018
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	<StructureSection load='5yac' size='340' side='right' caption='[[5yac]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='5yac' size='340' side='right' caption='[[5yac]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yac]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YAC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yac]] is a 1 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=5YAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YAC FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trm5b, PYRAB07390, PAB0505 ([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='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=5yac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yac OCA], [http://pdbe.org/5yac PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yac RCSB], [http://www.ebi.ac.uk/pdbsum/5yac PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yac 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=5yac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yac OCA], [http://pdbe.org/5yac PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yac RCSB], [http://www.ebi.ac.uk/pdbsum/5yac PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yac ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 5yac" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yac" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRNA methyltransferase\|TRNA methyltransferase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pyrab]]
	[[Category: Wu, J]]		[[Category: Wu, J]]
	[[Category: Xie, W]]		[[Category: Xie, W]]

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

2017-10-04T09:14:14Z

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

←Older revision

Revision as of 09:14, 4 October 2017

OCA: New page: ==Crystal structure of WT Trm5b from Pyrococcus abyssi== == Struc...

2017-10-04T09:14:11Z

New page: ==Crystal structure of WT Trm5b from Pyrococcus abyssi== <StructureSection load='5yac' size='340' side='right' caption='5yac, resolution 3.30Å' scene=''> == Struc...

New page

==Crystal structure of WT Trm5b from Pyrococcus abyssi==
<StructureSection load='5yac' size='340' side='right' caption='[[5yac]], [[Resolution|resolution]] 3.30Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5yac]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YAC FirstGlance]. <br>
</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=5yac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yac OCA], [http://pdbe.org/5yac PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yac RCSB], [http://www.ebi.ac.uk/pdbsum/5yac PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yac ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/TRM5B_PYRAB TRM5B_PYRAB]] Specifically methylates the N1 position of guanosine-37 in various tRNAs.<ref>PMID:20382657</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The wyosine hypermodification found exclusively at G37 of tRNAPhe in eukaryotes and archaea is a very complicated process involving multiple steps and enzymes, and the derivatives are essential for the maintenance of the reading frame during translation. In the archaea Pyrococcus abyssi, two key enzymes from the Trm5 family, named PaTrm5a and PaTrm5b respectively, start the process by forming N1-methylated guanosine (m1G37). In addition, PaTrm5a catalyzes the further methylation of C7 on 4-demethylwyosine (imG-14) to produce isowyosine (imG2) at the same position. The structural basis of the distinct methylation capacities and possible conformational changes during catalysis displayed by the Trm5 enzymes are poorly studied. Here we report the 3.3 A crystal structure of the mono-functional PaTrm5b, which shares 32% sequence identity with PaTrm5a. Interestingly, structural superposition reveals that the PaTrm5b protein exhibits an extended conformation similar to that of tRNA-bound Trm5b from Methanococcus jannaschii (MjTrm5b), but quite different from the open conformation of apo-PaTrm5a or well folded apo-MjTrm5b reported previously. Truncation of the N-terminal D1 domain leads to reduced tRNA binding as well as the methyltransfer activity of PaTrm5b. The differential positioning of the D1 domains from three reported Trm5 structures were rationalized, which could be attributable to the dissimilar inter-domain interactions and crystal packing patterns. This study expands our understanding on the methylation mechanism of the Trm5 enzymes and wyosine hypermodification.

The crystal structure of the Pyrococcus abyssi mono-functional methyltransferase PaTrm5b.,Wu J, Jia Q, Wu S, Zeng H, Sun Y, Wang C, Ge R, Xie W Biochem Biophys Res Commun. 2017 Sep 11. pii: S0006-291X(17)31798-9. doi:, 10.1016/j.bbrc.2017.09.038. PMID:28911863<ref>PMID:28911863</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5yac" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Wu, J]]
[[Category: Xie, W]]
[[Category: Open conformation]]
[[Category: Rna binding protein]]
[[Category: Trna maturation]]
[[Category: Trna methyltransferase]]
[[Category: Wyosine biosynthesis]]