6on3 - Revision history

OCA at 14:52, 13 March 2024

2024-03-13T14:52:31Z

←Older revision		Revision as of 14:52, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6on3' size='340' side='right'caption='[[6on3]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='6on3' size='340' side='right'caption='[[6on3]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6on3]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_15721 Atcc 15721~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ON3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ON3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6on3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sclerotialus Streptomyces sclerotialus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ON3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ON3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAH:3,4-DIHYDROXYPHENYLALANINE'>DAH</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.31Å</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=6on3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6on3 OCA], [~~http~~://pdbe.org/6on3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6on3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6on3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6on3 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAH:3,4-DIHYDROXYPHENYLALANINE'>DAH</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=6on3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6on3 OCA], [https://pdbe.org/6on3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6on3 RCSB], [https://www.ebi.ac.uk/pdbsum/6on3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6on3 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A5H1ZR51_9ACTN A0A5H1ZR51_9ACTN]
-	Extradiol dioxygenases are essential biocatalysts to breakdown catechols. The vicinal oxygen chelate (VOC) superfamily contains a large number of extradiol dioxygenases, most of which are found as part of catabolic pathways degrading a variety of natural and human-made aromatic rings. However, the VOC also contains an emerging class of biosynthetic dioxygenases. The L-3,4-dihydroxyphenylalanine (L-DOPA) extradiol dioxygenases are from pathways to various antibacterial or antitumor natural products, and their structural features are anticipated to be distinct from other VOC extradiol dioxygenases. Herein, we identified a new L-DOPA dioxygenase from the thermophilic bacterium Streptomyces sclerotialus (SsDDO), through a sequence and genome context analysis. The activity of SsDDO was kinetically characterized with L-DOPA using a UV-vis spectrophotometer and an oxygen electrode. The optimal temperature of the assay was 55 C, at which the Km and kcat of SsDDO were 110 +/~~- 10 muM and 2.0 +~~/~~- 0~~.~~1 s-1, respectively~~. We determined the de novo crystal structures of SsDDO in both the ligand-free form and as a substrate-bound complex, refined to 1.99 A and 2.31 A resolution, respectively. These structures reveal that SsDDO possesses a Form IV arrangement of betaalphabetabetabeta modules, the first characterization of this assembly from among the VOC/Type I extradiol dioxygenase protein family. EPR spectra of Fe-NO adducts for the resting and substrate-bound enzyme were obtained. This work contributes to our understanding of a growing class of topologically distinct VOC dioxygenases, and the obtained structural features will expand our knowledge of the extradiol cleavage reaction within the VOC superfamily.	+

-	Crystal Structures of L-DOPA Dioxygenase from Streptomyces Sclerotialus.,Wang Y, Shin I, Fu Y, Colabroy KL, Liu A Biochemistry. 2019 Jun 10. doi: 10.1021/acs.biochem.9b00396. PMID:31180203<ref>PMID:31180203</ref>	+	==See Also==
-		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6on3" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 15721]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Colabroy, K]]	+	[[Category: Streptomyces sclerotialus]]
-	[[Category: Fu, Y]]	+	[[Category: Colabroy K]]
-	[[Category: Liu, A]]	+	[[Category: Fu Y]]
-	[[Category: Shin, I]]	+	[[Category: Liu A]]
-	[[Category: Wang, Y]]	+	[[Category: Shin I]]
-	~~[[Category: Extradiol dioxygenase]]~~	+	[[Category: Wang Y]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Vincinal oxygen chelate superfamily~~]]	+

OCA at 09:08, 27 November 2019

2019-11-27T09:08:57Z

←Older revision		Revision as of 09:08, 27 November 2019
Line 3:		Line 3:
	<StructureSection load='6on3' size='340' side='right'caption='[[6on3]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='6on3' size='340' side='right'caption='[[6on3]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6on3]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ON3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ON3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6on3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_15721 Atcc 15721]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ON3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ON3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAH:3,4-DIHYDROXYPHENYLALANINE'>DAH</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAH:3,4-DIHYDROXYPHENYLALANINE'>DAH</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=6on3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6on3 OCA], [http://pdbe.org/6on3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6on3 RCSB], [http://www.ebi.ac.uk/pdbsum/6on3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6on3 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=6on3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6on3 OCA], [http://pdbe.org/6on3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6on3 RCSB], [http://www.ebi.ac.uk/pdbsum/6on3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6on3 ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 15721]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Colabroy, K]]		[[Category: Colabroy, K]]

OCA at 06:59, 26 June 2019

2019-06-26T06:59:23Z

←Older revision		Revision as of 06:59, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6on3 is ~~ON HOLD until Paper~~ Publication	+	==A substrate bound structure of L-DOPA dioxygenase from Streptomyces sclerotialus==
		+	<StructureSection load='6on3' size='340' side='right'caption='[[6on3]], [[Resolution\|resolution]] 2.31Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6on3]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ON3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ON3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAH:3,4-DIHYDROXYPHENYLALANINE'>DAH</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=6on3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6on3 OCA], [http://pdbe.org/6on3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6on3 RCSB], [http://www.ebi.ac.uk/pdbsum/6on3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6on3 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Extradiol dioxygenases are essential biocatalysts to breakdown catechols. The vicinal oxygen chelate (VOC) superfamily contains a large number of extradiol dioxygenases, most of which are found as part of catabolic pathways degrading a variety of natural and human-made aromatic rings. However, the VOC also contains an emerging class of biosynthetic dioxygenases. The L-3,4-dihydroxyphenylalanine (L-DOPA) extradiol dioxygenases are from pathways to various antibacterial or antitumor natural products, and their structural features are anticipated to be distinct from other VOC extradiol dioxygenases. Herein, we identified a new L-DOPA dioxygenase from the thermophilic bacterium Streptomyces sclerotialus (SsDDO), through a sequence and genome context analysis. The activity of SsDDO was kinetically characterized with L-DOPA using a UV-vis spectrophotometer and an oxygen electrode. The optimal temperature of the assay was 55 C, at which the Km and kcat of SsDDO were 110 +/- 10 muM and 2.0 +/- 0.1 s-1, respectively. We determined the de novo crystal structures of SsDDO in both the ligand-free form and as a substrate-bound complex, refined to 1.99 A and 2.31 A resolution, respectively. These structures reveal that SsDDO possesses a Form IV arrangement of betaalphabetabetabeta modules, the first characterization of this assembly from among the VOC/Type I extradiol dioxygenase protein family. EPR spectra of Fe-NO adducts for the resting and substrate-bound enzyme were obtained. This work contributes to our understanding of a growing class of topologically distinct VOC dioxygenases, and the obtained structural features will expand our knowledge of the extradiol cleavage reaction within the VOC superfamily.

-	~~Authors: Wang~~, Y., Shin, I., Fu, Y., Colabroy~~, K.~~, Liu, A.	+	Crystal Structures of L-DOPA Dioxygenase from Streptomyces Sclerotialus.,Wang Y, Shin I, Fu Y, Colabroy KL, Liu A Biochemistry. 2019 Jun 10. doi: 10.1021/acs.biochem.9b00396. PMID:31180203<ref>PMID:31180203</ref>

-	~~Description: A substrate bound structure~~ of L-~~DOPA dioxygenase from Streptomyces sclerotialus~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6on3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Colabroy, K]]		[[Category: Colabroy, K]]
	[[Category: Fu, Y]]		[[Category: Fu, Y]]
-	[[Category: Wang, Y]]
	[[Category: Liu, A]]		[[Category: Liu, A]]
	[[Category: Shin, I]]		[[Category: Shin, I]]
		+	[[Category: Wang, Y]]
		+	[[Category: Extradiol dioxygenase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Vincinal oxygen chelate superfamily]]

OCA at 03:58, 22 May 2019

2019-05-22T03:58:48Z

←Older revision		Revision as of 03:58, 22 May 2019
Line 5:		Line 5:
	Authors: Wang, Y., Shin, I., Fu, Y., Colabroy, K., Liu, A.		Authors: Wang, Y., Shin, I., Fu, Y., Colabroy, K., Liu, A.

-	Description: A substrate bound structure of L-DOPA ~~dioxygense~~ from Streptomyces sclerotialus	+	Description: A substrate bound structure of L-DOPA dioxygenase from Streptomyces sclerotialus
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Colabroy, K]]		[[Category: Colabroy, K]]
		+	[[Category: Fu, Y]]
	[[Category: Wang, Y]]		[[Category: Wang, Y]]
	[[Category: Liu, A]]		[[Category: Liu, A]]
-	[[Category: Fu, Y]]
	[[Category: Shin, I]]		[[Category: Shin, I]]

OCA: Protected "6on3" [edit=sysop:move=sysop]

2019-05-01T07:10:15Z

Protected "6on3" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:10, 1 May 2019

OCA: New page: '''Unreleased structure''' The entry 6on3 is ON HOLD until Paper Publication Authors: Wang, Y., Shin, I., Fu, Y., Colabroy, K., Liu, A. Description: A substrate bound structure of L-DO...

2019-05-01T07:10:13Z

New page: '''Unreleased structure''' The entry 6on3 is ON HOLD until Paper Publication Authors: Wang, Y., Shin, I., Fu, Y., Colabroy, K., Liu, A. Description: A substrate bound structure of L-DO...

New page

'''Unreleased structure'''

The entry 6on3 is ON HOLD until Paper Publication

Authors: Wang, Y., Shin, I., Fu, Y., Colabroy, K., Liu, A.

Description: A substrate bound structure of L-DOPA dioxygense from Streptomyces sclerotialus
[[Category: Unreleased Structures]]
[[Category: Colabroy, K]]
[[Category: Wang, Y]]
[[Category: Liu, A]]
[[Category: Fu, Y]]
[[Category: Shin, I]]