OCA at 07:38, 8 January 2020

OCA — Wed, 08 Jan 2020 07:38:21 GMT

←Older revision		Revision as of 07:38, 8 January 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6qsi is ~~ON HOLD until Paper~~ Publication	+	==Pseudomonas fluorescens Pf-5 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase==
		+	<StructureSection load='6qsi' size='340' side='right'caption='[[6qsi]], [[Resolution\|resolution]] 1.69Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6qsi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QSI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QSI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoylformate_decarboxylase Benzoylformate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.7 4.1.1.7] </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=6qsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qsi OCA], [http://pdbe.org/6qsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qsi RCSB], [http://www.ebi.ac.uk/pdbsum/6qsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qsi ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A thiamine diphosphate-dependent enzyme annotated as a benzoylformate decarboxylase is encoded by gene cluster ro02984-ro02986 in Rhodococcus jostii RHA1 previously shown to generate vanillin and 4-hydroxybenzaldehyde from lignin oxidation, and a closely related gene cluster is also found in the genome of Pseudomonas fluorescens Pf-5. Two hypotheses for possible pathways involving a thiamine diphosphate-dependent cleavage, either C-C cleavage of a ketol or diketone aryl C3 substrate or decarboxylation of an aryl C2 substrate, were investigated by expression and purification of the recombinant enzymes and expression of dehydrogenase and oxidase enzymes also found in the gene clusters. The ThDP-dependent enzymes showed no activity for cleavage of aryl C3 ketol or diketone substrates but showed activity for decarboxylation of benzoylformate and 4-hydroxybenzoylformate. A flavin-dependent oxidase encoded by gene ro02984 was found to oxidize either mandelic acid or phenylglyoxal. The crystal structure of the P. fluorescens decarboxylase enzyme was determined at 1.69 A resolution, showing similarity to structures of known benzoylformate decarboxylase enzymes. The P. fluorescens decarboxylase enzyme showed enhanced carboligase activity between vanillin and acetaldehyde, rationalized by the presence of alanine versus serine at residue 73 in the enzyme active site, which was investigated further by site-directed mutagenesis of this residue. A hypothesis for a pathway for degradation of aryl C2 fragments arising from oxidative cleavage of phenylcoumaran and diarylpropane structures in lignin is proposed.

-	~~Authors~~:	+	Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes from Rhodococcus jostii RHA1 and Pseudomonas fluorescens Pf-5 Involved in Degradation of Aryl C2 Lignin Degradation Fragments.,Wei Z, Wilkinson RC, Rashid GMM, Brown D, Fulop V, Bugg TDH Biochemistry. 2019 Dec 31;58(52):5281-5293. doi: 10.1021/acs.biochem.9b00177., Epub 2019 May 24. PMID:30946572<ref>PMID:30946572</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6qsi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Benzoylformate decarboxylase]]
		+	[[Category: Large Structures]]
		+	[[Category: Fulop, V]]
		+	[[Category: Wilkinson, R C]]
		+	[[Category: Lignin degradation]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pseudomonas fluorescens pf-5]]
		+	[[Category: Thaimine diphosphate]]

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

OCA — Wed, 27 Feb 2019 14:01:49 GMT

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

←Older revision

Revision as of 14:01, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qsi is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Feb 2019 14:01:47 GMT

New page: '''Unreleased structure''' The entry 6qsi is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6qsi is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]

6qsi - Revision history

OCA at 07:38, 8 January 2020

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

OCA: New page: '''Unreleased structure''' The entry 6qsi is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures