6vp5 - Revision history

OCA at 08:16, 11 October 2023

2023-10-11T08:16:26Z

←Older revision		Revision as of 08:16, 11 October 2023
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	==Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II), L-arginine, and 2OG==		==Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II), L-arginine, and 2OG==
-	<StructureSection load='6vp5' size='340' side='right'caption='[[6vp5]]' scene=''>	+	<StructureSection load='6vp5' size='340' side='right'caption='[[6vp5]], [[Resolution\|resolution]] 1.97Å' 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=6VP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VP5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vp5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_savastanoi_pv._phaseolicola Pseudomonas savastanoi pv. phaseolicola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VP5 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=6vp5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vp5 OCA], [https://pdbe.org/6vp5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vp5 RCSB], [https://www.ebi.ac.uk/pdbsum/6vp5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vp5 ProSAT]</span></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]] 1.97Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</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=6vp5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vp5 OCA], [https://pdbe.org/6vp5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vp5 RCSB], [https://www.ebi.ac.uk/pdbsum/6vp5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vp5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/EFE_PSESH EFE_PSESH] Simultaneously catalyzes two reactions, namely formation of ethylene and of succinate from 2-oxoglutarate, with a molar ratio of 2:1.<ref>PMID:1445291</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ethylene-forming enzyme (EFE) is an ambifunctional iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase. In its major (EF) reaction, it converts carbons 1, 2, and 5 of 2OG to CO(2) and carbons 3 and 4 to ethylene, a four-electron oxidation drastically different from the simpler decarboxylation of 2OG to succinate mediated by all other Fe/2OG enzymes. EFE also catalyzes a minor reaction, in which the normal decarboxylation is coupled to oxidation of l-arginine (a required activator for the EF pathway), resulting in its conversion to l-glutamate semialdehyde and guanidine. Here we show that, consistent with precedent, the l-Arg-oxidation (RO) pathway proceeds via an iron(IV)-oxo (ferryl) intermediate. Use of 5,5-[(2)H(2)]-l-Arg slows decay of the ferryl complex by >16-fold, implying that RO is initiated by hydrogen-atom transfer (HAT) from C5. That this large substrate deuterium kinetic isotope effect has no impact on the EF:RO partition ratio implies that the same ferryl intermediate cannot be on the EF pathway; the pathways must diverge earlier. Consistent with this conclusion, the variant enzyme bearing the Asp191Glu ligand substitution accumulates approximately 4 times as much of the ferryl complex as the wild-type enzyme and exhibits a approximately 40-fold diminished EF:RO partition ratio. The selective detriment of this nearly conservative substitution to the EF pathway implies that it has unusually stringent stereoelectronic requirements. An active-site, like-charge guanidinium pair, which involves the l-Arg substrate/activator and is unique to EFE among four crystallographically characterized l-Arg-modifying Fe/2OG oxygenases, may serve to selectively stabilize the transition state leading to the unique EF branch.
		+
		+	An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme.,Copeland RA, Davis KM, Shoda TKC, Blaesi EJ, Boal AK, Krebs C, Bollinger JM Jr J Am Chem Soc. 2021 Feb 10;143(5):2293-2303. doi: 10.1021/jacs.0c10923. Epub 2021 , Feb 1. PMID:33522811<ref>PMID:33522811</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vp5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pseudomonas savastanoi pv. phaseolicola]]
	[[Category: Boal AK]]		[[Category: Boal AK]]
	[[Category: Copeland RA]]		[[Category: Copeland RA]]
	[[Category: Davis KM]]		[[Category: Davis KM]]

OCA at 11:07, 3 February 2021

2021-02-03T11:07:02Z

←Older revision		Revision as of 11:07, 3 February 2021
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-	'''Unreleased structure'''

-	~~The entry 6vp5 is ON HOLD until Paper Publication~~	+	==Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II), L-arginine, and 2OG==
-		+	<StructureSection load='6vp5' size='340' side='right'caption='[[6vp5]]' scene=''>
-	~~Authors: Davis, K.M., Copeland, R.A., Boal, A.K.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VP5 FirstGlance]. <br>
-	~~Description:~~ Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II), L-arginine, and 2OG	+	</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=6vp5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vp5 OCA], [https://pdbe.org/6vp5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vp5 RCSB], [https://www.ebi.ac.uk/pdbsum/6vp5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vp5 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Davis~~, K.M]]	+	__TOC__
-	[[Category: Boal~~, A.K~~]]	+	</StructureSection>
-	[[Category: Copeland~~, R.A~~]]	+	[[Category: Large Structures]]
		+	[[Category: Boal AK]]
		+	[[Category: Copeland RA]]
		+	[[Category: Davis KM]]

OCA at 08:07, 26 February 2020

2020-02-26T08:07:52Z

←Older revision		Revision as of 08:07, 26 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6vp5 is ON HOLD	+	The entry 6vp5 is ON HOLD until Paper Publication

	Authors: Davis, K.M., Copeland, R.A., Boal, A.K.		Authors: Davis, K.M., Copeland, R.A., Boal, A.K.

OCA: Protected "6vp5" [edit=sysop:move=sysop]

2020-02-13T02:43:50Z

Protected "6vp5" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:43, 13 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vp5 is ON HOLD Authors: Davis, K.M., Copeland, R.A., Boal, A.K. Description: Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II), L...

2020-02-13T02:43:48Z

New page: '''Unreleased structure''' The entry 6vp5 is ON HOLD Authors: Davis, K.M., Copeland, R.A., Boal, A.K. Description: Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II), L...

New page

'''Unreleased structure'''

The entry 6vp5 is ON HOLD

Authors: Davis, K.M., Copeland, R.A., Boal, A.K.

Description: Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II), L-arginine, and 2OG
[[Category: Unreleased Structures]]
[[Category: Davis, K.M]]
[[Category: Boal, A.K]]
[[Category: Copeland, R.A]]