5vg2 - Revision history

OCA at 13:48, 4 October 2023

2023-10-04T13:48:10Z

←Older revision		Revision as of 13:48, 4 October 2023
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	<StructureSection load='5vg2' size='340' side='right'caption='[[5vg2]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='5vg2' size='340' side='right'caption='[[5vg2]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vg2]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Tetur Tetur~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VG2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VG2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vg2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Tetranychus_urticae Tetranychus urticae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VG2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 2.46Å</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=5vg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vg2 OCA], [~~http~~://pdbe.org/5vg2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vg2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vg2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vg2 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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=5vg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vg2 OCA], [https://pdbe.org/5vg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vg2 RCSB], [https://www.ebi.ac.uk/pdbsum/5vg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vg2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/T1K8P1_TETUR T1K8P1_TETUR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5vg2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vg2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Tetur]]
-	[[Category: Chruszcz, M]]
-	[[Category: Klapper, V]]
-	[[Category: Schlachter, C]]
-	[[Category: Catechol]]
-	[[Category: Dioxygenase]]
-	[[Category: Intradiol ring-cleavage]]
-	[[Category: Oxidoreductase]]
	[[Category: Tetranychus urticae]]		[[Category: Tetranychus urticae]]
		+	[[Category: Chruszcz M]]
		+	[[Category: Klapper V]]
		+	[[Category: Schlachter C]]

OCA at 06:29, 29 May 2019

2019-05-29T06:29:41Z

←Older revision		Revision as of 06:29, 29 May 2019
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	==Intradiol ring-cleavage Dioxygenase from Tetranychus urticae==		==Intradiol ring-cleavage Dioxygenase from Tetranychus urticae==
-	<StructureSection load='5vg2' size='340' side='right' caption='[[5vg2]], [[Resolution\|resolution]] 2.46Å' scene=''>	+	<StructureSection load='5vg2' size='340' side='right'caption='[[5vg2]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vg2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VG2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VG2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vg2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Tetur Tetur]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VG2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VG2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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=5vg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vg2 OCA], [http://pdbe.org/5vg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vg2 RCSB], [http://www.ebi.ac.uk/pdbsum/5vg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vg2 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=5vg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vg2 OCA], [http://pdbe.org/5vg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vg2 RCSB], [http://www.ebi.ac.uk/pdbsum/5vg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vg2 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Genome analyses of the polyphagous spider mite herbivore Tetranychus urticae (two-spotted spider mite) revealed the presence of a set of 17 genes that code for secreted proteins belonging to the "intradiol dioxygenase-like" subgroup. Phylogenetic analyses indicate that this novel enzyme family has been acquired by horizontal gene transfer. In order to better understand the role of these proteins in T. urticae, we have structurally and functionally characterized one paralog (tetur07g02040). It was demonstrated that this protein is indeed an intradiol ring-cleavage dioxygenase, as the enzyme is able to cleave catechol between two hydroxyl-groups using atmospheric dioxygen. The enzyme was characterized functionally and structurally. The active site of the T. urticae enzyme contains an Fe(3+) cofactor that is coordinated by two histidine and two tyrosine residues, an arrangement that is similar to those observed in bacterial homologs. However, the active site is significantly more solvent exposed than in bacterial proteins. Moreover, the mite enzyme is monomeric, while almost all structurally characterized bacterial homologs form oligomeric assemblies. Tetur07g02040 is not only the first spider mite dioxygenase that has been characterized at the molecular level, but is also the first structurally characterized intradiol ring-cleavage dioxygenase originating from a eukaryote.
		+
		+	Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch.,Schlachter CR, Daneshian L, Amaya J, Klapper V, Wybouw N, Borowski T, Van Leeuwen T, Grbic V, Grbic M, Makris TM, Chruszcz M Insect Biochem Mol Biol. 2019 Apr;107:19-30. doi: 10.1016/j.ibmb.2018.12.001., Epub 2018 Dec 5. PMID:30529144<ref>PMID:30529144</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vg2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Tetur]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]
	[[Category: Klapper, V]]		[[Category: Klapper, V]]

OCA at 13:46, 11 April 2018

2018-04-11T13:46:31Z

←Older revision		Revision as of 13:46, 11 April 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5vg2 is ~~ON HOLD~~	+	==Intradiol ring-cleavage Dioxygenase from Tetranychus urticae==
-		+	<StructureSection load='5vg2' size='340' side='right' caption='[[5vg2]], [[Resolution\|resolution]] 2.46Å' scene=''>
-	~~Authors~~: ~~Schlachter~~, C., ~~Klapper~~, V., ~~Chruszcz~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vg2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VG2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VG2 FirstGlance]. <br>
-	~~Description: Intradiol ring-cleavage Dioxygenase from Tetranychus urticae~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5vg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vg2 OCA], [http://pdbe.org/5vg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vg2 RCSB], [http://www.ebi.ac.uk/pdbsum/5vg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vg2 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chruszcz, M]]
	[[Category: Klapper, V]]		[[Category: Klapper, V]]
-	[[Category: Chruszcz, M]]
	[[Category: Schlachter, C]]		[[Category: Schlachter, C]]
		+	[[Category: Catechol]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Intradiol ring-cleavage]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Tetranychus urticae]]

OCA at 12:15, 27 April 2017

2017-04-27T12:15:30Z

←Older revision		Revision as of 12:15, 27 April 2017
Line 3:		Line 3:
	The entry 5vg2 is ON HOLD		The entry 5vg2 is ON HOLD

-	Authors: ~~Caleb~~ Schlachter, ~~Vincent~~ Klapper, ~~Maksymilian~~ Chruszcz	+	Authors: Schlachter, C., Klapper, V., Chruszcz, M.

	Description: Intradiol ring-cleavage Dioxygenase from Tetranychus urticae		Description: Intradiol ring-cleavage Dioxygenase from Tetranychus urticae
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Caleb Schlachter, Vincent~~ Klapper, ~~Maksymilian~~ Chruszcz]]	+	[[Category: Klapper, V]]
		+	[[Category: Chruszcz, M]]
		+	[[Category: Schlachter, C]]

OCA: Protected "5vg2" [edit=sysop:move=sysop]

2017-04-19T11:23:53Z

Protected "5vg2" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:23, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vg2 is ON HOLD Authors: Caleb Schlachter, Vincent Klapper, Maksymilian Chruszcz Description: Intradiol ring-cleavage Dioxygenase from Tetranychus ...

2017-04-19T11:23:52Z

New page: '''Unreleased structure''' The entry 5vg2 is ON HOLD Authors: Caleb Schlachter, Vincent Klapper, Maksymilian Chruszcz Description: Intradiol ring-cleavage Dioxygenase from Tetranychus ...

New page

'''Unreleased structure'''

The entry 5vg2 is ON HOLD

Authors: Caleb Schlachter, Vincent Klapper, Maksymilian Chruszcz

Description: Intradiol ring-cleavage Dioxygenase from Tetranychus urticae
[[Category: Unreleased Structures]]
[[Category: Caleb Schlachter, Vincent Klapper, Maksymilian Chruszcz]]