5hji - Revision history

OCA at 07:39, 9 August 2023

2023-08-09T07:39:03Z

←Older revision		Revision as of 07:39, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='5hji' size='340' side='right'caption='[[5hji]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5hji' size='340' side='right'caption='[[5hji]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hji]] 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=5HJI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HJI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hji]] 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=5HJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HJI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADN:ADENOSINE'>ADN</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hjj\|5hjj]]~~, [[~~5hjm~~\|~~5hjm]], [[5hjk\|5hjk~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</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=5hji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hji OCA], [https://pdbe.org/5hji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hji RCSB], [https://www.ebi.ac.uk/pdbsum/5hji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hji 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~~://proteopedia.org/fgij/fg.htm?mol=5hji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hji OCA], [~~http~~://pdbe.org/5hji PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hji RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hji PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hji 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 ==
Line 29:		Line 27:
	</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: Adenosine]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Sam]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trm5a]]~~	+
-	~~[[Category: Trna modification~~]]	+

OCA at 08:18, 27 May 2020

2020-05-27T08:18:28Z

←Older revision		Revision as of 08:18, 27 May 2020
Line 1:		Line 1:

	==Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine==		==Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine==
-	<StructureSection load='5hji' size='340' side='right' caption='[[5hji]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5hji' size='340' side='right'caption='[[5hji]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hji]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HJI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HJI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hji]] 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=5HJI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HJI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hjj\|5hjj]], [[5hjm\|5hjm]], [[5hjk\|5hjk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hjj\|5hjj]], [[5hjm\|5hjm]], [[5hjk\|5hjk]]</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=5hji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hji OCA], [http://pdbe.org/5hji PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hji RCSB], [http://www.ebi.ac.uk/pdbsum/5hji PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hji ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5hji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hji OCA], [http://pdbe.org/5hji PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hji RCSB], [http://www.ebi.ac.uk/pdbsum/5hji PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hji ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5hji" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5hji" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRNA methyltransferase 3D structures\|TRNA methyltransferase 3D structures]]
	== 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 17:40, 19 October 2016

2016-10-19T17:40:12Z

←Older revision		Revision as of 17:40, 19 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hji is ~~ON HOLD~~ ~~until Jan 13 2018~~	+	==Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine==
		+	<StructureSection load='5hji' size='340' side='right' caption='[[5hji]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hji]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HJI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hjj\|5hjj]], [[5hjm\|5hjm]], [[5hjk\|5hjk]]</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=5hji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hji OCA], [http://pdbe.org/5hji PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hji RCSB], [http://www.ebi.ac.uk/pdbsum/5hji PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hji 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	tRNA methyltransferase Trm5 catalyses the transfer of a methyl group from S-adenosyl-L-methionine to G37 in eukaryotes and archaea. The N1-methylated guanosine is the product of the initial step of the wyosine hypermodification, which is essential for the maintenance of the reading frame during translation. As a unique member of this enzyme family, Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4-demethylwyosine at position 37 to produce isowyosine, but the mechanism for the double methylation is poorly understood. Here we report four crystal structures of PaTrm5a ranging from 1.7- to 2.3-A, in the apo form or in complex with various SAM analogues. These structures reveal that Asp243 specifically recognises the base moiety of SAM at the active site. Interestingly, the protein in our structures all displays an extended conformation, quite different from the well-folded conformation of Trm5b from Methanocaldococcus jannaschii reported previously, despite their similar overall architectures. To rule out the possibilities of crystallisation artefacts, we conducted the fluorescence resonance energy transfer (FRET) experiments. The FRET data suggested that PaTrm5a adopts a naturally extended conformation in solution, and therefore the open conformation is a genuine state of PaTrm5a.

-	~~Authors: Xie, W~~., Wang, C., Jia, Q.	+	Crystal structures of the bifunctional tRNA methyltransferase Trm5a.,Wang C, Jia Q, Chen R, Wei Y, Li J, Ma J, Xie W Sci Rep. 2016 Sep 15;6:33553. doi: 10.1038/srep33553. PMID:27629654<ref>PMID:27629654</ref>

-	~~Description: Crystal Structure~~ of ~~Pyrococcus abyssi Trm5a complexed with adenosine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Xie, W]]~~	+	<div class="pdbe-citations 5hji" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Jia, Q]]		[[Category: Jia, Q]]
	[[Category: Wang, C]]		[[Category: Wang, C]]
		+	[[Category: Xie, W]]
		+	[[Category: Adenosine]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Sam]]
		+	[[Category: Transferase]]
		+	[[Category: Trm5a]]
		+	[[Category: Trna modification]]

OCA at 00:45, 28 January 2016

2016-01-28T00:45:52Z

←Older revision		Revision as of 00:45, 28 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hji is ON HOLD	+	The entry 5hji is ON HOLD until Jan 13 2018

-	Authors: Xie, W, Wang, C, Jia, Q	+	Authors: Xie, W., Wang, C., Jia, Q.

	Description: Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine		Description: Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Xie, W, Wang, C~~, Jia, Q~~]]	+	[[Category: Xie, W]]
		+	[[Category: Jia, Q]]
		+	[[Category: Wang, C]]

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

2016-01-20T15:35:49Z

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

←Older revision

Revision as of 15:35, 20 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hji is ON HOLD Authors: Xie, W, Wang, C, Jia, Q Description: Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine [[Category: Unr...

2016-01-20T15:35:47Z

New page: '''Unreleased structure''' The entry 5hji is ON HOLD Authors: Xie, W, Wang, C, Jia, Q Description: Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine [[Category: Unr...

New page

'''Unreleased structure'''

The entry 5hji is ON HOLD

Authors: Xie, W, Wang, C, Jia, Q

Description: Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine
[[Category: Unreleased Structures]]
[[Category: Xie, W, Wang, C, Jia, Q]]