5jmv - Revision history

OCA at 18:58, 20 September 2023

2023-09-20T18:58:59Z

←Older revision		Revision as of 18:58, 20 September 2023
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	==Crystal structure of mjKae1-pfuPcc1 complex==		==Crystal structure of mjKae1-pfuPcc1 complex==
-	<StructureSection load='5jmv' size='340' side='right' caption='[[5jmv]], [[Resolution\|resolution]] 3.39Å' scene=''>	+	<StructureSection load='5jmv' size='340' side='right'caption='[[5jmv]], [[Resolution\|resolution]] 3.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jmv]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Metja Metja~~] and [~~http~~://en.wikipedia.org/wiki/~~Pyrfu Pyrfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JMV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jmv]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661] and [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JMV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 3.3864696Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~MJ1130 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=243232 METJA]), PF2011 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=186497 PYRFU])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5jmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmv OCA], [~~http~~://pdbe.org/5jmv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jmv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jmv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmv 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=5jmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmv OCA], [https://pdbe.org/5jmv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jmv RCSB], [https://www.ebi.ac.uk/pdbsum/5jmv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KAE1B_METJA KAE1B_METJA]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is a component of the KEOPS complex that is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. The Kae1 domain likely plays a direct catalytic role in this reaction (By similarity). The Bud32 domain probably displays kinase activity that regulates Kae1 function. In vitro, exhibits low ATPase activity, but does not bind DNA and does not have endonuclease activity.[HAMAP-Rule:MF_01447]<ref>PMID:18951093</ref>	+	[https://www.uniprot.org/uniprot/KAE1B_METJA KAE1B_METJA] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is a component of the KEOPS complex that is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. The Kae1 domain likely plays a direct catalytic role in this reaction (By similarity). The Bud32 domain probably displays kinase activity that regulates Kae1 function. In vitro, exhibits low ATPase activity, but does not bind DNA and does not have endonuclease activity.[HAMAP-Rule:MF_01447]<ref>PMID:18951093</ref>
	<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: ~~Metja~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Pyrfu~~]]	+	[[Category: Methanocaldococcus jannaschii DSM 2661]]
-	[[Category: ~~Sicheri, F~~]]	+	[[Category: Pyrococcus furiosus DSM 3638]]
-	[[Category: ~~Wan, L~~]]	+	[[Category: Sicheri F]]
-	[[Category: ~~Transferase]]~~	+	[[Category: Wan L]]
-	~~[[Category: Trna modification~~]]	+

OCA at 10:03, 22 November 2017

2017-11-22T10:03:37Z

←Older revision		Revision as of 10:03, 22 November 2017
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	<StructureSection load='5jmv' size='340' side='right' caption='[[5jmv]], [[Resolution\|resolution]] 3.39Å' scene=''>		<StructureSection load='5jmv' size='340' side='right' caption='[[5jmv]], [[Resolution\|resolution]] 3.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jmv]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JMV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jmv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja] and [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JMV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1130 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA]), PF2011 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=5jmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmv OCA], [http://pdbe.org/5jmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jmv RCSB], [http://www.ebi.ac.uk/pdbsum/5jmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmv 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=5jmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmv OCA], [http://pdbe.org/5jmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jmv RCSB], [http://www.ebi.ac.uk/pdbsum/5jmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmv ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Metja]]
		+	[[Category: Pyrfu]]
	[[Category: Sicheri, F]]		[[Category: Sicheri, F]]
	[[Category: Wan, L]]		[[Category: Wan, L]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Trna modification]]		[[Category: Trna modification]]

OCA at 10:07, 13 July 2016

2016-07-13T10:07:54Z

←Older revision		Revision as of 10:07, 13 July 2016
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-	==~~Structure~~ of ~~a tRNA modification~~ complex==	+	==Crystal structure of mjKae1-pfuPcc1 complex==
	<StructureSection load='5jmv' size='340' side='right' caption='[[5jmv]], [[Resolution\|resolution]] 3.39Å' scene=''>		<StructureSection load='5jmv' size='340' side='right' caption='[[5jmv]], [[Resolution\|resolution]] 3.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 02:17, 13 July 2016

2016-07-13T02:17:27Z

←Older revision		Revision as of 02:17, 13 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jmv is ~~ON HOLD~~	+	==Structure of a tRNA modification complex==
		+	<StructureSection load='5jmv' size='340' side='right' caption='[[5jmv]], [[Resolution\|resolution]] 3.39Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jmv]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JMV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmv OCA], [http://pdbe.org/5jmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jmv RCSB], [http://www.ebi.ac.uk/pdbsum/5jmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KAE1B_METJA KAE1B_METJA]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is a component of the KEOPS complex that is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. The Kae1 domain likely plays a direct catalytic role in this reaction (By similarity). The Bud32 domain probably displays kinase activity that regulates Kae1 function. In vitro, exhibits low ATPase activity, but does not bind DNA and does not have endonuclease activity.[HAMAP-Rule:MF_01447]<ref>PMID:18951093</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	KEOPS is an ancient protein complex required for the biosynthesis of N6-threonylcarbamoyladenosine (t6A), a universally conserved tRNA modification found on all ANN-codon recognizing tRNAs. KEOPS consist minimally of four essential subunits, namely the proteins Kae1, Bud32, Cgi121 and Pcc1, with yeast possessing the fifth essential subunit Gon7. Bud32, Cgi121, Pcc1 and Gon7 appear to have evolved to regulate the central t6A biosynthesis function of Kae1, but their precise function and mechanism of action remains unclear. Pcc1, in particular, binds directly to Kae1 and by virtue of its ability to form dimers in solution and in crystals, Pcc1 was inferred to function as a dimerization module for Kae1 and therefore KEOPS. We now present a 3.4 A crystal structure of a dimeric Kae1-Pcc1 complex providing direct evidence that Pcc1 can bind and dimerize Kae1. Further biophysical analysis of a complete archaeal KEOPS complex reveals that Pcc1 facilitates KEOPS dimerization in vitro Interestingly, while Pcc1-mediated dimerization of KEOPS is required to support the growth of yeast, it is dispensable for t6A biosynthesis by archaeal KEOPS in vitro, raising the question of how precisely Pcc1-mediated dimerization impacts cellular biology.

-	~~Authors~~:	+	Structural and functional characterization of KEOPS dimerization by Pcc1 and its role in t6A biosynthesis.,Wan LC, Pillon MC, Thevakumaran N, Sun Y, Chakrabartty A, Guarne A, Kurinov I, Durocher D, Sicheri F Nucleic Acids Res. 2016 Jun 14. pii: gkw542. PMID:27302132<ref>PMID:27302132</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jmv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Sicheri, F]]
		+	[[Category: Wan, L]]
		+	[[Category: Transferase]]
		+	[[Category: Trna modification]]

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

2016-05-15T15:36:11Z

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

←Older revision

Revision as of 15:36, 15 May 2016

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

2016-05-15T15:36:10Z

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

New page

'''Unreleased structure'''

The entry 5jmv is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]