6hsq - Revision history

OCA at 11:38, 24 January 2024

OCA — Wed, 24 Jan 2024 11:38:44 GMT

←Older revision		Revision as of 11:38, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6hsq' size='340' side='right'caption='[[6hsq]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='6hsq' size='340' side='right'caption='[[6hsq]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hsq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HSQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HSQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hsq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Psychromonas_ingrahamii_37 Psychromonas ingrahamii 37]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HSQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HSQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.46Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/3-dehydroquinate_dehydratase 3-dehydroquinate dehydratase]~~, ~~with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.10 4.2.1.10]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hsq OCA], [~~http~~://pdbe.org/6hsq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6hsq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6hsq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6hsq 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=6hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hsq OCA], [https://pdbe.org/6hsq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hsq RCSB], [https://www.ebi.ac.uk/pdbsum/6hsq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hsq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AROQ_PSYIN AROQ_PSYIN]] Catalyzes a trans-dehydration via an enolate intermediate.	+	[https://www.uniprot.org/uniprot/AROQ_PSYIN AROQ_PSYIN] Catalyzes a trans-dehydration via an enolate intermediate.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	3-Dehydroquinate dehydratase (DHQase) catalyzes the conversion of 3-dehydroquinic acid to 3-dehydroshikimic acid of the shikimate pathway. In this study, 3180 prokaryotic genomes were examined and 459 DHQase sequences were retrieved. Based on sequence analysis and their original hosts, 38 DHQase genes were selected for chemical synthesis. The selected DHQases were translated into new DNA sequences according to the genetic codon usage bias by both Escherichia coli and Corynebacterium glutamicum. The new DNA sequences were customized for synthetic biological applications by adding Biobrick adapters at both ends and by removal of any related restriction endonuclease sites. The customized DHQase genes were successfully expressed in E. coli, and functional DHQases were obtained. Kinetic parameters of Km, kcat, and Vmax of DHQases were determined with a newly established high-throughput method for DHQase activity assay. Results showed that DHQases possessed broad strength of substrate affinities and catalytic capacities. In addition to the DHQase kinetic diversities, this study generated a DHQase library with known catalytic constants that could be applied to design artificial modules of shikimate pathway for metabolic engineering and synthetic biology.	+

-	Unraveling the kinetic diversity of microbial 3-dehydroquinate dehydratases of shikimate pathway.,Liu C, Liu YM, Sun QL, Jiang CY, Liu SJ AMB Express. 2015 Feb 1;5:7. doi: 10.1186/s13568-014-0087-y. eCollection 2015. PMID:25852984<ref>PMID:25852984</ref>	+	==See Also==
-		+	*[[Dehydroquinase 3D structures\|Dehydroquinase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6hsq" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 3-dehydroquinate dehydratase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lapthorn, A J~~]]	+	[[Category: Psychromonas ingrahamii 37]]
-	[[Category: ~~Roszak, A W~~]]	+	[[Category: Lapthorn AJ]]
-	[[Category: ~~Biosynthetic protein]]~~	+	[[Category: Roszak AW]]
-	~~[[Category: Dehydratase]]~~	+
-	~~[[Category: Shikimate pathway~~]]	+

OCA at 06:44, 23 October 2019

OCA — Wed, 23 Oct 2019 06:44:53 GMT

←Older revision		Revision as of 06:44, 23 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6hsq is ~~ON HOLD until Oct 01 2020~~	+	==The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 crystal form 1==
		+	<StructureSection load='6hsq' size='340' side='right'caption='[[6hsq]], [[Resolution\|resolution]] 1.46Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6hsq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HSQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HSQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-dehydroquinate_dehydratase 3-dehydroquinate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.10 4.2.1.10] </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=6hsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hsq OCA], [http://pdbe.org/6hsq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hsq RCSB], [http://www.ebi.ac.uk/pdbsum/6hsq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hsq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AROQ_PSYIN AROQ_PSYIN]] Catalyzes a trans-dehydration via an enolate intermediate.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	3-Dehydroquinate dehydratase (DHQase) catalyzes the conversion of 3-dehydroquinic acid to 3-dehydroshikimic acid of the shikimate pathway. In this study, 3180 prokaryotic genomes were examined and 459 DHQase sequences were retrieved. Based on sequence analysis and their original hosts, 38 DHQase genes were selected for chemical synthesis. The selected DHQases were translated into new DNA sequences according to the genetic codon usage bias by both Escherichia coli and Corynebacterium glutamicum. The new DNA sequences were customized for synthetic biological applications by adding Biobrick adapters at both ends and by removal of any related restriction endonuclease sites. The customized DHQase genes were successfully expressed in E. coli, and functional DHQases were obtained. Kinetic parameters of Km, kcat, and Vmax of DHQases were determined with a newly established high-throughput method for DHQase activity assay. Results showed that DHQases possessed broad strength of substrate affinities and catalytic capacities. In addition to the DHQase kinetic diversities, this study generated a DHQase library with known catalytic constants that could be applied to design artificial modules of shikimate pathway for metabolic engineering and synthetic biology.

-	~~Authors~~:	+	Unraveling the kinetic diversity of microbial 3-dehydroquinate dehydratases of shikimate pathway.,Liu C, Liu YM, Sun QL, Jiang CY, Liu SJ AMB Express. 2015 Feb 1;5:7. doi: 10.1186/s13568-014-0087-y. eCollection 2015. PMID:25852984<ref>PMID:25852984</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6hsq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 3-dehydroquinate dehydratase]]
		+	[[Category: Large Structures]]
		+	[[Category: Lapthorn, A J]]
		+	[[Category: Roszak, A W]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Dehydratase]]
		+	[[Category: Shikimate pathway]]

OCA at 06:12, 17 October 2018

OCA — Wed, 17 Oct 2018 06:12:54 GMT

←Older revision		Revision as of 06:12, 17 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6hsq is ON HOLD	+	The entry 6hsq is ON HOLD until Oct 01 2020

-	Authors: ~~Lapthorn, A.J., Roszak, A.W.~~	+	Authors:

-	Description: ~~The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Roszak, A.W]]
-	[[Category: Lapthorn, A.J]]

OCA: Protected "6hsq" [edit=sysop:move=sysop]

OCA — Wed, 10 Oct 2018 06:14:18 GMT

Protected "6hsq" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:14, 10 October 2018

OCA: New page: '''Unreleased structure''' The entry 6hsq is ON HOLD Authors: Lapthorn, A.J., Roszak, A.W. Description: The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 ...

OCA — Wed, 10 Oct 2018 06:14:16 GMT

New page: '''Unreleased structure''' The entry 6hsq is ON HOLD Authors: Lapthorn, A.J., Roszak, A.W. Description: The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 ...

New page

'''Unreleased structure'''

The entry 6hsq is ON HOLD

Authors: Lapthorn, A.J., Roszak, A.W.

Description: The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37
[[Category: Unreleased Structures]]
[[Category: Roszak, A.W]]
[[Category: Lapthorn, A.J]]