5axm - Revision history

OCA at 15:50, 8 November 2023

OCA — Wed, 08 Nov 2023 15:50:55 GMT

←Older revision		Revision as of 15:50, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5axm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_acetivorans Methanosarcina acetivorans] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AXM FirstGlance]. <br>		<table><tr><td colspan='2'>[[5axm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_acetivorans Methanosarcina acetivorans] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.21Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5axm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axm OCA], [https://pdbe.org/5axm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5axm RCSB], [https://www.ebi.ac.uk/pdbsum/5axm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5axm 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=5axm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axm OCA], [https://pdbe.org/5axm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5axm RCSB], [https://www.ebi.ac.uk/pdbsum/5axm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5axm ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:30, 31 May 2023

OCA — Wed, 31 May 2023 06:30:14 GMT

←Older revision		Revision as of 06:30, 31 May 2023
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	<StructureSection load='5axm' size='340' side='right'caption='[[5axm]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='5axm' size='340' side='right'caption='[[5axm]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5axm]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_35395 Atcc 35395~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5axm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_acetivorans Methanosarcina acetivorans] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene><~~/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=5axm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axm OCA], [https://pdbe.org/5axm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5axm RCSB], [https://www.ebi.ac.uk/pdbsum/5axm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5axm ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5axk\|5axk]], [[5axl\|5axl]], [[5axn\|5axn]]~~</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=5axm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axm OCA], [~~http~~://pdbe.org/5axm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5axm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5axm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5axm ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1C7D1G9_9EURY A0A1C7D1G9_9EURY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 35395]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kato, K~~]]	+	[[Category: Methanosarcina acetivorans]]
-	[[Category: ~~Kimura, S~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Suzuki, T~~]]	+	[[Category: Kato K]]
-	[[Category: ~~Yao, M~~]]	+	[[Category: Kimura S]]
-	[[Category: ~~Yu, J~~]]	+	[[Category: Suzuki T]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Yao M]]
-	[[Category: ~~Transferase-rna complex~~]]	+	[[Category: Yu J]]

OCA at 06:57, 10 July 2019

OCA — Wed, 10 Jul 2019 06:57:13 GMT

←Older revision		Revision as of 06:57, 10 July 2019
Line 1:		Line 1:

	==Crystal structure of Thg1 like protein (TLP) with tRNA(Phe)==		==Crystal structure of Thg1 like protein (TLP) with tRNA(Phe)==
-	<StructureSection load='5axm' size='340' side='right' caption='[[5axm]], [[Resolution\|resolution]] 2.21Å' scene=''>	+	<StructureSection load='5axm' size='340' side='right'caption='[[5axm]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5axm]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5axm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35395 Atcc 35395]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AXM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 35395]]
		+	[[Category: Large Structures]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
	[[Category: Kimura, S]]		[[Category: Kimura, S]]

OCA at 04:07, 4 August 2016

OCA — Thu, 04 Aug 2016 04:07:01 GMT

←Older revision		Revision as of 04:07, 4 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5axm is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Thg1 like protein (TLP) with tRNA(Phe)==
		+	<StructureSection load='5axm' size='340' side='right' caption='[[5axm]], [[Resolution\|resolution]] 2.21Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5axm]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AXM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5axk\|5axk]], [[5axl\|5axl]], [[5axn\|5axn]]</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=5axm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axm OCA], [http://pdbe.org/5axm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5axm RCSB], [http://www.ebi.ac.uk/pdbsum/5axm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5axm ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5'-end of truncated transfer RNA (tRNA) species in a Watson-Crick template-dependent manner. The reaction proceeds in two steps: the activation of the 5'-end by adenosine 5'-triphosphate (ATP)/guanosine 5'-triphosphate (GTP), followed by nucleotide addition. Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3'-5' direction. The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg(2+) ions, and the two reactions are executed at the same reaction center in a stepwise fashion. When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3'-OH of the incoming nucleotide and the 5'-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. That the 3'-5' elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution. Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNA(His)-specific G-1 addition enzyme. Each tRNA(His) binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible beta-hairpin. Furthermore, mutational analyses show that tRNA(His) is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.

-	~~Authors~~:	+	Template-dependent nucleotide addition in the reverse (3'-5') direction by Thg1-like protein.,Kimura S, Suzuki T, Chen M, Kato K, Yu J, Nakamura A, Tanaka I, Yao M Sci Adv. 2016 Mar 25;2(3):e1501397. doi: 10.1126/sciadv.1501397. eCollection 2016, Mar. PMID:27051866<ref>PMID:27051866</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5axm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kato, K]]
		+	[[Category: Kimura, S]]
		+	[[Category: Suzuki, T]]
		+	[[Category: Yao, M]]
		+	[[Category: Yu, J]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-rna complex]]

OCA at 10:59, 15 May 2016

OCA — Sun, 15 May 2016 10:59:58 GMT

←Older revision		Revision as of 10:59, 15 May 2016
Line 3:		Line 3:
	The entry 5axm is ON HOLD until Paper Publication		The entry 5axm is ON HOLD until Paper Publication

-	Authors: ~~Kimura, S., Suzuki, T., Yu, J., Kato, K., Yao, M.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kimura, S]]
-	[[Category: Yao, M]]
-	[[Category: Kato, K]]
-	[[Category: Suzuki, T]]
-	[[Category: Yu, J]]

OCA at 09:59, 16 December 2015

OCA — Wed, 16 Dec 2015 09:59:17 GMT

←Older revision		Revision as of 09:59, 16 December 2015
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kimura, S]]		[[Category: Kimura, S]]
-	[[Category: Yu, J]]
	[[Category: Yao, M]]		[[Category: Yao, M]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
	[[Category: Suzuki, T]]		[[Category: Suzuki, T]]
		+	[[Category: Yu, J]]

OCA at 08:31, 9 September 2015

OCA — Wed, 09 Sep 2015 08:31:58 GMT

←Older revision		Revision as of 08:31, 9 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5axm is ON HOLD	+	The entry 5axm is ON HOLD until Paper Publication

-	Authors: Kimura, S., Suzuki, T., Kato, K., Yao, M.	+	Authors: Kimura, S., Suzuki, T., Yu, J., Kato, K., Yao, M.

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kimura, S]]		[[Category: Kimura, S]]
		+	[[Category: Yu, J]]
	[[Category: Yao, M]]		[[Category: Yao, M]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
	[[Category: Suzuki, T]]		[[Category: Suzuki, T]]

OCA at 12:25, 12 August 2015

OCA — Wed, 12 Aug 2015 12:25:17 GMT

←Older revision		Revision as of 12:25, 12 August 2015
Line 3:		Line 3:
	The entry 5axm is ON HOLD		The entry 5axm is ON HOLD

-	Authors: ~~Shoko~~, K., ~~Tateki~~, S., ~~Koji~~, K., ~~Min~~, Y.	+	Authors: Kimura, S., Suzuki, T., Kato, K., Yao, M.

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Tateki~~, S]]	+	[[Category: Kimura, S]]
-	[[Category: ~~Shoko~~, K]]	+	[[Category: Yao, M]]
-	[[Category: ~~Min~~, Y]]	+	[[Category: Kato, K]]
-	[[Category: ~~Koji~~, K]]	+	[[Category: Suzuki, T]]

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

OCA — Wed, 05 Aug 2015 17:47:36 GMT

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

←Older revision

Revision as of 17:47, 5 August 2015

OCA: New page: '''Unreleased structure''' The entry 5axm is ON HOLD Authors: Shoko, K., Tateki, S., Koji, K., Min, Y. Description: Category: Unreleased Structures Category: Tateki, S [[Categ...

OCA — Wed, 05 Aug 2015 17:47:34 GMT

New page: '''Unreleased structure''' The entry 5axm is ON HOLD Authors: Shoko, K., Tateki, S., Koji, K., Min, Y. Description: Category: Unreleased Structures Category: Tateki, S [[Categ...

New page

'''Unreleased structure'''

The entry 5axm is ON HOLD

Authors: Shoko, K., Tateki, S., Koji, K., Min, Y.

Description:
[[Category: Unreleased Structures]]
[[Category: Tateki, S]]
[[Category: Shoko, K]]
[[Category: Min, Y]]
[[Category: Koji, K]]