4wq4 - Revision history

OCA at 07:20, 7 April 2023

OCA — Fri, 07 Apr 2023 07:20:52 GMT

←Older revision		Revision as of 07:20, 7 April 2023
Line 3:		Line 3:
	<StructureSection load='4wq4' size='340' side='right'caption='[[4wq4]], [[Resolution\|resolution]] 2.33Å' scene=''>		<StructureSection load='4wq4' size='340' side='right'caption='[[4wq4]], [[Resolution\|resolution]] 2.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wq4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WQ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4WQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wq4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WQ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tsaD, gcp, ygjD, b3064, JW3036 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), tsaB, yeaZ, b1807, JW1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4wq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wq4 OCA], [https://pdbe.org/4wq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wq4 RCSB], [https://www.ebi.ac.uk/pdbsum/4wq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wq4 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/N(6)-L-threonylcarbamoyladenine_synthase N(6)-L-threonylcarbamoyladenine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.99.4 2.6.99.4] </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=4wq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wq4 OCA], [~~http~~://pdbe.org/4wq4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4wq4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4wq4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4wq4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TSAD_ECOLI TSAD_ECOLI]] 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 probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. May also be involved in the metabolism of glycated proteins, but does not show sialoglycoprotease activity against glycophorin A.<ref>PMID:20824107</ref> <ref>PMID:21183954</ref> <ref>PMID:22378793</ref> [[http://www.uniprot.org/uniprot/TSAB_ECOLI TSAB_ECOLI]] 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 probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD. In fact, can act as a protease that specifically degrades TsaD in vitro; therefore TsaB may post-translationally regulate cellular pools of TsaD via proteolytic degradation. Does not show sialoglycoprotease activity against glycophorin A.<ref>PMID:19376873</ref> <ref>PMID:22378793</ref>	+	[https://www.uniprot.org/uniprot/TSAD_ECOLI TSAD_ECOLI] 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 probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. May also be involved in the metabolism of glycated proteins, but does not show sialoglycoprotease activity against glycophorin A.<ref>PMID:20824107</ref> <ref>PMID:21183954</ref> <ref>PMID:22378793</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: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Collinet, B]]	+	[[Category: Collinet B]]
-	[[Category: Zhang, W]]	+	[[Category: Zhang W]]
-	~~[[Category: Glu12ala]]~~	+
-	~~[[Category: Heterodimer]]~~	+
-	~~[[Category: T6a]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Ygjd-yeaz~~]]	+

OCA at 09:13, 23 May 2019

OCA — Thu, 23 May 2019 09:13:15 GMT

←Older revision		Revision as of 09:13, 23 May 2019
Line 1:		Line 1:
		+
	==E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP==		==E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP==
-	<StructureSection load='4wq4' size='340' side='right' caption='[[4wq4]], [[Resolution\|resolution]] 2.33Å' scene=''>	+	<StructureSection load='4wq4' size='340' side='right'caption='[[4wq4]], [[Resolution\|resolution]] 2.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wq4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wq4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WQ4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tsaD, gcp, ygjD, b3064, JW3036 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), tsaB, yeaZ, b1807, JW1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N(6)-L-threonylcarbamoyladenine_synthase N(6)-L-threonylcarbamoyladenine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.99.4 2.6.99.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N(6)-L-threonylcarbamoyladenine_synthase N(6)-L-threonylcarbamoyladenine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.99.4 2.6.99.4] </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=4wq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wq4 RCSB], [http://www.ebi.ac.uk/pdbsum/4wq4 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=4wq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wq4 OCA], [http://pdbe.org/4wq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wq4 RCSB], [http://www.ebi.ac.uk/pdbsum/4wq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wq4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		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 4wq4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Collinet, B]]		[[Category: Collinet, B]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]

OCA at 16:41, 28 January 2015

OCA — Wed, 28 Jan 2015 16:41:27 GMT

←Older revision		Revision as of 16:41, 28 January 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP==
		+	<StructureSection load='4wq4' size='340' side='right' caption='[[4wq4]], [[Resolution\|resolution]] 2.33Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4wq4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WQ4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N(6)-L-threonylcarbamoyladenine_synthase N(6)-L-threonylcarbamoyladenine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.99.4 2.6.99.4] </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=4wq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wq4 RCSB], [http://www.ebi.ac.uk/pdbsum/4wq4 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TSAD_ECOLI TSAD_ECOLI]] 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 probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. May also be involved in the metabolism of glycated proteins, but does not show sialoglycoprotease activity against glycophorin A.<ref>PMID:20824107</ref> <ref>PMID:21183954</ref> <ref>PMID:22378793</ref> [[http://www.uniprot.org/uniprot/TSAB_ECOLI TSAB_ECOLI]] 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 probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD. In fact, can act as a protease that specifically degrades TsaD in vitro; therefore TsaB may post-translationally regulate cellular pools of TsaD via proteolytic degradation. Does not show sialoglycoprotease activity against glycophorin A.<ref>PMID:19376873</ref> <ref>PMID:22378793</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The essential and universal N6-threonylcarbamoyladenosine (t6A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (TsaB), YjeE (TsaE) and YrdC (TsaC) proteins are necessary and sufficient for the in vitro biosynthesis of t6A, using tRNA, ATP, L-threonine and bicarbonate as substrates. YrdC synthesizes the short-lived L-threonylcarbamoyladenylate (TCA), and YgjD, YeaZ and YjeE cooperate to transfer the L-threonylcarbamoyl-moiety from TCA onto adenosine at position 37 of substrate tRNA. We determined the crystal structure of the heterodimer YgjD-YeaZ at 2.3 A, revealing the presence of an unexpected molecule of ADP bound at an atypical site situated at the YgjD-YeaZ interface. We further showed that the ATPase activity of YjeE is strongly activated by the YgjD-YeaZ heterodimer. We established by binding experiments and SAXS data analysis that YgjD-YeaZ and YjeE form a compact ternary complex only in presence of ATP. The formation of the ternary YgjD-YeaZ-YjeE complex is required for the in vitro biosynthesis of t6A but not its ATPase activity.

-	The ~~entry 4wq4~~ is ~~ON HOLD~~	+	The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.,Zhang W, Collinet B, Perrochia L, Durand D, van Tilbeurgh H Nucleic Acids Res. 2015 Jan 10. pii: gku1397. PMID:25578970<ref>PMID:25578970</ref>

-	~~Authors: Zhang~~, W.~~, Collinet, B~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Collinet, B]]		[[Category: Collinet, B]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]
		+	[[Category: Glu12ala]]
		+	[[Category: Heterodimer]]
		+	[[Category: T6a]]
		+	[[Category: Transferase]]
		+	[[Category: Ygjd-yeaz]]

OCA at 19:51, 24 December 2014

OCA — Wed, 24 Dec 2014 19:51:33 GMT

←Older revision		Revision as of 19:51, 24 December 2014
Line 6:		Line 6:

	Description: E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP		Description: E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP
		+	[[Category: Unreleased Structures]]
		+	[[Category: Collinet, B]]
		+	[[Category: Zhang, W]]

OCA: Protected "4wq4" [edit=sysop:move=sysop]

OCA — Wed, 29 Oct 2014 10:34:54 GMT

Protected "4wq4" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:34, 29 October 2014

OCA: New page: '''Unreleased structure''' The entry 4wq4 is ON HOLD Authors: Zhang, W., Collinet, B. Description: E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP

OCA — Wed, 29 Oct 2014 10:34:53 GMT

New page: '''Unreleased structure''' The entry 4wq4 is ON HOLD Authors: Zhang, W., Collinet, B. Description: E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP

New page

'''Unreleased structure'''

The entry 4wq4 is ON HOLD

Authors: Zhang, W., Collinet, B.

Description: E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP