7ney - Revision history

OCA at 12:34, 1 February 2024

2024-02-01T12:34:06Z

←Older revision		Revision as of 12:34, 1 February 2024
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	<StructureSection load='7ney' size='340' side='right'caption='[[7ney]], [[Resolution\|resolution]] 1.74Å' scene=''>		<StructureSection load='7ney' size='340' side='right'caption='[[7ney]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ney]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Hypai Hypai~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ney]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_atroviride_IMI_206040 Trichoderma atroviride IMI 206040]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4LU:1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-TETRAMETHYL-9,11-DIOXO-2,3,8,9,10,11-HEXAHYDRO-7H-QUINOLINO[1,8-FG]PTERIDIN-12-IUM-7-YL)-D-RIBITOL'>4LU</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.74Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDC1, TRIATDRAFT_53567 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=452589 HYPAI])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4LU:1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-TETRAMETHYL-9,11-DIOXO-2,3,8,9,10,11-HEXAHYDRO-7H-QUINOLINO[1,8-FG]PTERIDIN-12-IUM-7-YL)-D-RIBITOL'>4LU</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phenacrylate_decarboxylase Phenacrylate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.102 4.1.1.102] </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=7ney FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ney OCA], [https://pdbe.org/7ney PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ney RCSB], [https://www.ebi.ac.uk/pdbsum/7ney PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ney 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=7ney FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ney OCA], [https://pdbe.org/7ney PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ney RCSB], [https://www.ebi.ac.uk/pdbsum/7ney PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ney ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/G9NLP8_HYPAI G9NLP8_HYPAI]] Catalyzes the reversible decarboxylation of aromatic carboxylic acids like ferulic acid, p-coumaric acid or cinnamic acid, producing the corresponding vinyl derivatives 4-vinylphenol, 4-vinylguaiacol, and styrene, respectively, which play the role of aroma metabolites.[HAMAP-Rule:MF_03196]	+	[https://www.uniprot.org/uniprot/G9NLP8_HYPAI G9NLP8_HYPAI] Catalyzes the reversible decarboxylation of aromatic carboxylic acids like ferulic acid, p-coumaric acid or cinnamic acid, producing the corresponding vinyl derivatives 4-vinylphenol, 4-vinylguaiacol, and styrene, respectively, which play the role of aroma metabolites.[HAMAP-Rule:MF_03196]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Hypai]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Phenacrylate decarboxylase~~]]	+	[[Category: Trichoderma atroviride IMI 206040]]
-	[[Category: Leys, D]]	+	[[Category: Leys D]]
-	[[Category: Saaret, A]]	+	[[Category: Saaret A]]
-	~~[[Category: Decarboxylase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Prfmn~~]]	+

OCA at 05:54, 6 October 2021

2021-10-06T05:54:56Z

←Older revision		Revision as of 05:54, 6 October 2021
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	==Structure of T. atroviride Fdc wild-type (TaFdc) in complex with prFMN==		==Structure of T. atroviride Fdc wild-type (TaFdc) in complex with prFMN==
-	<StructureSection load='7ney' size='340' side='right'caption='[[7ney]]' scene=''>	+	<StructureSection load='7ney' size='340' side='right'caption='[[7ney]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ney]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hypai Hypai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEY FirstGlance]. <br>
-	</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=7ney FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ney OCA], [https://pdbe.org/7ney PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ney RCSB], [https://www.ebi.ac.uk/pdbsum/7ney PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ney ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4LU:1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-TETRAMETHYL-9,11-DIOXO-2,3,8,9,10,11-HEXAHYDRO-7H-QUINOLINO[1,8-FG]PTERIDIN-12-IUM-7-YL)-D-RIBITOL'>4LU</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FDC1, TRIATDRAFT_53567 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=452589 HYPAI])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phenacrylate_decarboxylase Phenacrylate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.102 4.1.1.102] </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=7ney FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ney OCA], [https://pdbe.org/7ney PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ney RCSB], [https://www.ebi.ac.uk/pdbsum/7ney PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ney ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/G9NLP8_HYPAI G9NLP8_HYPAI]] Catalyzes the reversible decarboxylation of aromatic carboxylic acids like ferulic acid, p-coumaric acid or cinnamic acid, producing the corresponding vinyl derivatives 4-vinylphenol, 4-vinylguaiacol, and styrene, respectively, which play the role of aroma metabolites.[HAMAP-Rule:MF_03196]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Isobutene is a high value gaseous alkene used as fuel additive and a chemical building block. As an alternative to fossil fuel derived isobutene, we here develop a modified mevalonate pathway for the production of isobutene from glucose in vivo. The final step in the pathway consists of the decarboxylation of 3-methylcrotonic acid, catalysed by an evolved ferulic acid decarboxylase (Fdc) enzyme. Fdc belongs to the prFMN-dependent UbiD enzyme family that catalyses reversible decarboxylation of (hetero)aromatic acids or acrylic acids with extended conjugation. Following a screen of an Fdc library for inherent 3-methylcrotonic acid decarboxylase activity, directed evolution yields variants with up to an 80-fold increase in activity. Crystal structures of the evolved variants reveal that changes in the substrate binding pocket are responsible for increased selectivity. Solution and computational studies suggest that isobutene cycloelimination is rate limiting and strictly dependent on presence of the 3-methyl group.
		+
		+	Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production.,Saaret A, Villiers B, Stricher F, Anissimova M, Cadillon M, Spiess R, Hay S, Leys D Nat Commun. 2021 Sep 6;12(1):5300. doi: 10.1038/s41467-021-25598-0. PMID:34489427<ref>PMID:34489427</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ney" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hypai]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Leys D]]	+	[[Category: Phenacrylate decarboxylase]]
-	[[Category: Saaret A]]	+	[[Category: Leys, D]]
		+	[[Category: Saaret, A]]
		+	[[Category: Decarboxylase]]
		+	[[Category: Lyase]]
		+	[[Category: Prfmn]]

OCA at 10:20, 4 August 2021

2021-08-04T10:20:39Z

←Older revision		Revision as of 10:20, 4 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7ney ~~is ON HOLD until Paper Publication~~	+	==Structure of T. atroviride Fdc wild-type (TaFdc) in complex with prFMN==
-		+	<StructureSection load='7ney' size='340' side='right'caption='[[7ney]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEY FirstGlance]. <br>
-	~~Description~~:	+	</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=7ney FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ney OCA], [https://pdbe.org/7ney PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ney RCSB], [https://www.ebi.ac.uk/pdbsum/7ney PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ney ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Leys D]]
		+	[[Category: Saaret A]]

OCA at 14:53, 10 March 2021

2021-03-10T14:53:35Z

←Older revision		Revision as of 14:53, 10 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ney is ON HOLD	+	The entry 7ney is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7ney" [edit=sysop:move=sysop]

2021-02-17T08:52:45Z

Protected "7ney" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:52, 17 February 2021

OCA: New page: '''Unreleased structure''' The entry 7ney is ON HOLD Authors: Description: Category: Unreleased Structures

2021-02-17T08:52:44Z

New page: '''Unreleased structure''' The entry 7ney is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7ney is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]