4k25 - Revision history

OCA at 11:37, 30 November 2022

OCA — Wed, 30 Nov 2022 11:37:08 GMT

←Older revision		Revision as of 11:37, 30 November 2022
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	==Crystal Structure of yeast Qri7 homodimer==		==Crystal Structure of yeast Qri7 homodimer==
-	<StructureSection load='4k25' size='340' side='right' caption='[[4k25]], [[Resolution\|resolution]] 2.88Å' scene=''>	+	<StructureSection load='4k25' size='340' side='right'caption='[[4k25]], [[Resolution\|resolution]] 2.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4k25]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K25 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4K25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4k25]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K25 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:~~ZINC+ION~~'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</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=4k25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k25 OCA], [https://pdbe.org/4k25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k25 RCSB], [https://www.ebi.ac.uk/pdbsum/4k25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k25 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">QRI7, YDL104C, D2366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4k25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k25 OCA], [~~http~~://pdbe.org/4k25 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4k25 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4k25 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4k25 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/QRI7_YEAST QRI7_YEAST]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. Involved in mitochondrial genome maintenance.<ref>PMID:21183954</ref> <ref>PMID:21285948</ref>	+	[https://www.uniprot.org/uniprot/QRI7_YEAST QRI7_YEAST] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. Involved in mitochondrial genome maintenance.<ref>PMID:21183954</ref> <ref>PMID:21285948</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baker's yeast~~]]	+	[[Category: Large Structures]]
-	[[Category: Mao~~, D Y~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Neculai, D]]	+	[[Category: Mao DY]]
-	[[Category: Sicheri, F]]	+	[[Category: Neculai D]]
-	[[Category: Wan, L]]	+	[[Category: Sicheri F]]
-	~~[[Category: Askha-fold]]~~	+	[[Category: Wan L]]
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Mitochondria]]~~	+
-	~~[[Category: N6-threonylcarbamoylation enzyme]]~~	+
-	~~[[Category: Rna and metabolite binding~~]]	+

OCA at 05:03, 5 August 2016

OCA — Fri, 05 Aug 2016 05:03:10 GMT

←Older revision		Revision as of 05:03, 5 August 2016
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		+
	==Crystal Structure of yeast Qri7 homodimer==		==Crystal Structure of yeast Qri7 homodimer==
	<StructureSection load='4k25' size='340' side='right' caption='[[4k25]], [[Resolution\|resolution]] 2.88Å' scene=''>		<StructureSection load='4k25' size='340' side='right' caption='[[4k25]], [[Resolution\|resolution]] 2.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4k25]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4k25]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K25 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">QRI7, YDL104C, D2366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 ~~Saccharomyces cerevisiae S288c~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">QRI7, YDL104C, D2366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4k25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k25 RCSB], [http://www.ebi.ac.uk/pdbsum/4k25 PDBsum]</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=4k25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k25 OCA], [http://pdbe.org/4k25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k25 RCSB], [http://www.ebi.ac.uk/pdbsum/4k25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k25 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4k25" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae s288c~~]]	+	[[Category: Baker's yeast]]
	[[Category: Mao, D Y]]		[[Category: Mao, D Y]]
	[[Category: Neculai, D]]		[[Category: Neculai, D]]

OCA at 15:59, 25 December 2014

OCA — Thu, 25 Dec 2014 15:59:11 GMT

←Older revision		Revision as of 15:59, 25 December 2014
Line 8:		Line 8:
	<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=4k25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k25 RCSB], [http://www.ebi.ac.uk/pdbsum/4k25 PDBsum]</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=4k25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k25 RCSB], [http://www.ebi.ac.uk/pdbsum/4k25 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/QRI7_YEAST QRI7_YEAST]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. Involved in mitochondrial genome maintenance.<ref>PMID:21183954</ref> <ref>PMID:21285948</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 15:34, 21 December 2014

OCA — Sun, 21 Dec 2014 15:34:30 GMT

←Older revision		Revision as of 15:34, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4k25~~\| ~~PDB~~=4k25 \| ~~SCENE~~= }}	+	==Crystal Structure of yeast Qri7 homodimer==
-	===~~Crystal Structure of yeast Qri7 homodimer~~===	+	<StructureSection load='4k25' size='340' side='right' caption='[[4k25]], [[Resolution\|resolution]] 2.88Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23620299}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4k25]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K25 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">QRI7, YDL104C, D2366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Saccharomyces cerevisiae S288c])</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=4k25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k25 RCSB], [http://www.ebi.ac.uk/pdbsum/4k25 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The universally conserved Kae1/Qri7/YgjD and Sua5/YrdC protein families have been implicated in growth, telomere homeostasis, transcription and the N6-threonylcarbamoylation (t6A) of tRNA, an essential modification required for translational fidelity by the ribosome. In bacteria, YgjD orthologues operate in concert with the bacterial-specific proteins YeaZ and YjeE, whereas in archaeal and eukaryotic systems, Kae1 operates as part of a larger macromolecular assembly called KEOPS with Bud32, Cgi121, Gon7 and Pcc1 subunits. Qri7 orthologues function in the mitochondria and may represent the most primitive member of the Kae1/Qri7/YgjD protein family. In accordance with previous findings, we confirm that Qri7 complements Kae1 function and uncover that Qri7 complements the function of all KEOPS subunits in growth, t6A biosynthesis and, to a partial degree, telomere maintenance. These observations suggest that Kae1 provides a core essential function that other subunits within KEOPS have evolved to support. Consistent with this inference, Qri7 alone is sufficient for t6A biosynthesis with Sua5 in vitro. In addition, the 2.9 A crystal structure of Qri7 reveals a simple homodimer arrangement that is supplanted by the heterodimerization of YgjD with YeaZ in bacteria and heterodimerization of Kae1 with Pcc1 in KEOPS. The partial complementation of telomere maintenance by Qri7 hints that KEOPS has evolved novel functions in higher organisms.

-	~~==Function==~~	+	Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system.,Wan LC, Mao DY, Neculai D, Strecker J, Chiovitti D, Kurinov I, Poda G, Thevakumaran N, Yuan F, Szilard RK, Lissina E, Nislow C, Caudy AA, Durocher D, Sicheri F Nucleic Acids Res. 2013 Apr 25. PMID:23620299<ref>PMID:23620299</ref>
-	~~[[http://www.uniprot.org/uniprot/QRI7_YEAST QRI7_YEAST]] Required for the formation~~ of a ~~threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine~~. ~~Involved in mitochondrial genome maintenance~~.~~<ref>~~PMID:~~21183954</ref>~~ <ref>PMID:~~21285948~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4k25]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4K25 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023620299</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae s288c]]		[[Category: Saccharomyces cerevisiae s288c]]
-	[[Category: Mao, D Y.]]	+	[[Category: Mao, D Y]]
-	[[Category: Neculai, D.]]	+	[[Category: Neculai, D]]
-	[[Category: Sicheri, F.]]	+	[[Category: Sicheri, F]]
-	[[Category: Wan, L.]]	+	[[Category: Wan, L]]
	[[Category: Askha-fold]]		[[Category: Askha-fold]]
	[[Category: Biosynthetic protein]]		[[Category: Biosynthetic protein]]

OCA at 19:22, 7 August 2013

OCA — Wed, 07 Aug 2013 19:22:05 GMT

←Older revision		Revision as of 19:22, 7 August 2013
Line 10:		Line 10:

	==Reference==		==Reference==
-	<references group="xtra"/><references/>	+	<ref group="xtra">PMID:023620299</ref><references group="xtra"/><references/>
	[[Category: Saccharomyces cerevisiae s288c]]		[[Category: Saccharomyces cerevisiae s288c]]
	[[Category: Mao, D Y.]]		[[Category: Mao, D Y.]]

OCA at 07:42, 8 May 2013

OCA — Wed, 08 May 2013 07:42:40 GMT

←Older revision		Revision as of 07:42, 8 May 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4k25\| PDB=4k25 \| SCENE= }}
		+	===Crystal Structure of yeast Qri7 homodimer===
		+	{{ABSTRACT_PUBMED_23620299}}

-	~~The entry 4k25 is ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/QRI7_YEAST QRI7_YEAST]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. Involved in mitochondrial genome maintenance.<ref>PMID:21183954</ref> <ref>PMID:21285948</ref>

-	~~Authors~~: ~~Neculai, D~~.~~, Wan, L~~.~~, Mao, D~~.Y.~~, Sicheri, F~~.	+	==About this Structure==
		+	[[4k25]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K25 OCA].

-	~~Description~~: ~~Crystal Structure of yeast Qri7 homodimer~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Saccharomyces cerevisiae s288c]]
		+	[[Category: Mao, D Y.]]
		+	[[Category: Neculai, D.]]
		+	[[Category: Sicheri, F.]]
		+	[[Category: Wan, L.]]
		+	[[Category: Askha-fold]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Mitochondria]]
		+	[[Category: N6-threonylcarbamoylation enzyme]]
		+	[[Category: Rna and metabolite binding]]

OCA at 07:10, 2 May 2013

OCA — Thu, 02 May 2013 07:10:47 GMT

←Older revision		Revision as of 07:10, 2 May 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4k25 is ON HOLD	+	The entry 4k25 is ON HOLD until Paper Publication

	Authors: Neculai, D., Wan, L., Mao, D.Y., Sicheri, F.		Authors: Neculai, D., Wan, L., Mao, D.Y., Sicheri, F.

	Description: Crystal Structure of yeast Qri7 homodimer		Description: Crystal Structure of yeast Qri7 homodimer

OCA: Protected "4k25" [edit=sysop:move=sysop]

OCA — Wed, 17 Apr 2013 20:06:26 GMT

Protected "4k25" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:06, 17 April 2013

OCA: New page: '''Unreleased structure''' The entry 4k25 is ON HOLD Authors: Neculai, D., Wan, L., Mao, D.Y., Sicheri, F. Description: Crystal Structure of yeast Qri7 homodimer

OCA — Wed, 17 Apr 2013 20:06:25 GMT

New page: '''Unreleased structure''' The entry 4k25 is ON HOLD Authors: Neculai, D., Wan, L., Mao, D.Y., Sicheri, F. Description: Crystal Structure of yeast Qri7 homodimer

New page

'''Unreleased structure'''

The entry 4k25 is ON HOLD

Authors: Neculai, D., Wan, L., Mao, D.Y., Sicheri, F.

Description: Crystal Structure of yeast Qri7 homodimer