8h0m - Revision history

OCA at 18:15, 29 November 2023

OCA — Wed, 29 Nov 2023 18:15:09 GMT

←Older revision		Revision as of 18:15, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8h0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Duganella_sp._ZLP-XI Duganella sp. ZLP-XI]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8H0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8H0M FirstGlance]. <br>		<table><tr><td colspan='2'>[[8h0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Duganella_sp._ZLP-XI Duganella sp. ZLP-XI]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8H0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8H0M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2EH:(2S)-2-ETHYLHEXAN-1-OL'>2EH</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 1.702Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2EH:(2S)-2-ETHYLHEXAN-1-OL'>2EH</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=8h0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h0m OCA], [https://pdbe.org/8h0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h0m RCSB], [https://www.ebi.ac.uk/pdbsum/8h0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h0m 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=8h0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h0m OCA], [https://pdbe.org/8h0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h0m RCSB], [https://www.ebi.ac.uk/pdbsum/8h0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h0m ProSAT]</span></td></tr>
	</table>		</table>

OCA at 20:34, 12 April 2023

OCA — Wed, 12 Apr 2023 20:34:53 GMT

←Older revision		Revision as of 20:34, 12 April 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8h0m is ~~ON HOLD~~	+	==Crystal structure of VioD==
		+	<StructureSection load='8h0m' size='340' side='right'caption='[[8h0m]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8h0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Duganella_sp._ZLP-XI Duganella sp. ZLP-XI]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8H0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8H0M FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2EH:(2S)-2-ETHYLHEXAN-1-OL'>2EH</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=8h0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h0m OCA], [https://pdbe.org/8h0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h0m RCSB], [https://www.ebi.ac.uk/pdbsum/8h0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h0m ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A024AX32_9BURK A0A024AX32_9BURK]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Violacein is a pigment synthesized by gram-negative bacteria with various biological activities such as antimicrobial, antiviral, and anticancer activities. VioD is a key oxygenase converting protodeoxyviolaceinic acid to protoviolaceinic acid in violacein biosynthesis. To elucidate the catalytic mechanism of VioD, here, we resolved two crystal structures of VioD, a binary complex structure containing VioD and a FAD and a ternary complex structure composed of VioD, a FAD and a 2-ethyl-1-hexanol (EHN). Structural analysis revealed a deep funnel like binding pocket with wide entrance, this pocket is positively charged. The EHN is located at the deep bottom of the binding pocket near isoalloxazine ring. Further docking simulation help us to propose the mechanism of the hydroxylation of the substrate catalyzed by VioD. Bioinformatic analysis suggested and emphasized the importance of the conserved residues involved in substrate binding. Our results provide a structural basis for the catalytic mechanism of VioD.

-	~~Authors: Xu~~, M., ~~Ran~~, T., ~~Wang~~, W.	+	Structural basis for substrate binding and catalytic mechanism of the key enzyme VioD in the violacein synthesis pathway.,Xu M, Xu D, Gao M, Zhuang X, Wang W, Sun B, Ran T Proteins. 2023 Mar 4. doi: 10.1002/prot.26484. PMID:36869636<ref>PMID:36869636</ref>

-	~~Description: Crystal structure~~ of ~~VioD~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Wang, W~~]]	+	<div class="pdbe-citations 8h0m" style="background-color:#fffaf0;"></div>
-	[[Category: Ran, T]]	+	== References ==
-	[[Category: Xu, M]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Duganella sp. ZLP-XI]]
		+	[[Category: Large Structures]]
		+	[[Category: Ran T]]
		+	[[Category: Wang W]]
		+	[[Category: Xu M]]

OCA: Protected "8h0m" [edit=sysop:move=sysop]

OCA — Wed, 19 Oct 2022 17:40:26 GMT

Protected "8h0m" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:40, 19 October 2022

OCA: New page: '''Unreleased structure''' The entry 8h0m is ON HOLD Authors: Xu, M., Ran, T., Wang, W. Description: Crystal structure of VioD Category: Unreleased Structures Category: Wang, W...

OCA — Wed, 19 Oct 2022 17:40:22 GMT

New page: '''Unreleased structure''' The entry 8h0m is ON HOLD Authors: Xu, M., Ran, T., Wang, W. Description: Crystal structure of VioD Category: Unreleased Structures Category: Wang, W...

New page

'''Unreleased structure'''

The entry 8h0m is ON HOLD

Authors: Xu, M., Ran, T., Wang, W.

Description: Crystal structure of VioD
[[Category: Unreleased Structures]]
[[Category: Wang, W]]
[[Category: Ran, T]]
[[Category: Xu, M]]