5v2x - Revision history

OCA at 13:40, 4 October 2023

OCA — Wed, 04 Oct 2023 13:40:34 GMT

←Older revision		Revision as of 13:40, 4 October 2023
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	<StructureSection load='5v2x' size='340' side='right'caption='[[5v2x]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5v2x' size='340' side='right'caption='[[5v2x]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v2x]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Psesh Psesh~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V2X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V2X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v2x]] is a 2 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=5V2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V2X FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=AKG:2~~-~~OXOGLUTARIC+ACID'>AKG</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]] 1.847Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5v2t\|5v2t]], [[5v2u\|5v2u]], [[5v2v\|5v2v]], [[5v2y\|5v2y]], [[5v2z\|5v2z]], [[5v31\|5v31]], [[5v32\|5v32]], [[5v34\|5v34]]~~<~~/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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">efe ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=319 PSESH])~~</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=5v2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v2x OCA], [https://pdbe.org/5v2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v2x RCSB], [https://www.ebi.ac.uk/pdbsum/5v2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v2x 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=5v2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v2x OCA], [~~http~~://pdbe.org/5v2x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v2x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v2x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v2x ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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>	+	[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Psesh~~]]	+	[[Category: Pseudomonas savastanoi pv. phaseolicola]]
-	[[Category: Fellner, M]]	+	[[Category: Fellner M]]
-	[[Category: Hausinger~~, R P~~]]	+	[[Category: Hausinger RP]]
-	[[Category: Hu, J]]	+	[[Category: Hu J]]
-	[[Category: Martinez, S]]	+	[[Category: Martinez S]]
-	~~[[Category: 2-ketoglutaric acid]]~~	+
-	~~[[Category: 2-oxoglutaric acid]]~~	+
-	~~[[Category: Alpha-ketoglutaric acid]]~~	+
-	~~[[Category: Ethylene biosynthesis]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxoglutaric acid~~]]	+

OCA at 09:27, 1 January 2020

OCA — Wed, 01 Jan 2020 09:27:09 GMT

←Older revision		Revision as of 09:27, 1 January 2020
Line 1:		Line 1:

	==Ethylene forming enzyme in complex with manganese and 2-oxoglutarate==		==Ethylene forming enzyme in complex with manganese and 2-oxoglutarate==
-	<StructureSection load='5v2x' size='340' side='right' caption='[[5v2x]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5v2x' size='340' side='right'caption='[[5v2x]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v2x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V2X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v2x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Psesh Psesh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V2X FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v2t\|5v2t]], [[5v2u\|5v2u]], [[5v2v\|5v2v]], [[5v2y\|5v2y]], [[5v2z\|5v2z]], [[5v31\|5v31]], [[5v32\|5v32]], [[5v34\|5v34]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v2t\|5v2t]], [[5v2u\|5v2u]], [[5v2v\|5v2v]], [[5v2y\|5v2y]], [[5v2z\|5v2z]], [[5v31\|5v31]], [[5v32\|5v32]], [[5v34\|5v34]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">efe ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=319 PSESH])</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=5v2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v2x OCA], [http://pdbe.org/5v2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v2x RCSB], [http://www.ebi.ac.uk/pdbsum/5v2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v2x 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=5v2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v2x OCA], [http://pdbe.org/5v2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v2x RCSB], [http://www.ebi.ac.uk/pdbsum/5v2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v2x ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Psesh]]
	[[Category: Fellner, M]]		[[Category: Fellner, M]]
	[[Category: Hausinger, R P]]		[[Category: Hausinger, R P]]

OCA at 06:08, 17 August 2017

OCA — Thu, 17 Aug 2017 06:08:05 GMT

←Older revision		Revision as of 06:08, 17 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5v2x is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Ethylene forming enzyme in complex with manganese and 2-oxoglutarate==
		+	<StructureSection load='5v2x' size='340' side='right' caption='[[5v2x]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v2x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V2X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v2t\|5v2t]], [[5v2u\|5v2u]], [[5v2v\|5v2v]], [[5v2y\|5v2y]], [[5v2z\|5v2z]], [[5v31\|5v31]], [[5v32\|5v32]], [[5v34\|5v34]]</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=5v2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v2x OCA], [http://pdbe.org/5v2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v2x RCSB], [http://www.ebi.ac.uk/pdbsum/5v2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v2x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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 ==
		+	The ethylene-forming enzyme (EFE) from Pseudomonas syringae pv. phaseolicola PK2 is a member of the mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily. EFE converts 2OG into ethylene plus three CO2 molecules while also catalyzing the C5 hydroxylation of L-arginine (L-Arg) driven by the oxidative decarboxylation of 2OG to form succinate and CO2. Here we report eleven X-ray crystal structures of EFE that provide insight into the mechanisms of these two reactions. Binding of 2OG in the absence of L-Arg resulted in predominantly monodentate metal coordination, distinct from the typical bidentate metal-binding species observed in other family members. Subsequent addition of L-Arg resulted in compression of the active site, a conformational change of the carboxylate side chain metal ligand to allow for hydrogen bonding with the substrate, and creation of a twisted peptide bond involving this carboxylate and the following tyrosine residue. A reconfiguration of 2OG achieves bidentate metal coordination. The dioxygen binding site is located on the metal face opposite to that facing L-Arg, thus requiring reorientation of the generated ferryl species to catalyze L-Arg hydroxylation. Notably, a phenylalanyl side chain pointing towards the metal may hinder such a ferryl flip and promote ethylene formation. Extensive site-directed mutagenesis studies supported the importance of this phenylalanine and confirmed the essential residues used for substrate binding and catalysis. The structural and functional characterization described here suggests that conversion of 2OG to ethylene, atypical among Fe(II)/2OG oxygenases, is facilitated by the binding of L-Arg which leads to an altered positioning of the carboxylate metal ligand, a resulting twisted peptide bond, and the off-line geometry for dioxygen coordination.

-	~~Authors~~:	+	Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist.,Martinez S, Fellner M, Herr CQ, Ritchie A, Hu J, Hausinger RP J Am Chem Soc. 2017 Aug 5. doi: 10.1021/jacs.7b06186. PMID:28780854<ref>PMID:28780854</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5v2x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fellner, M]]
		+	[[Category: Hausinger, R P]]
		+	[[Category: Hu, J]]
		+	[[Category: Martinez, S]]
		+	[[Category: 2-ketoglutaric acid]]
		+	[[Category: 2-oxoglutaric acid]]
		+	[[Category: Alpha-ketoglutaric acid]]
		+	[[Category: Ethylene biosynthesis]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxoglutaric acid]]

OCA: Protected "5v2x" [edit=sysop:move=sysop]

OCA — Wed, 15 Mar 2017 19:40:43 GMT

Protected "5v2x" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:40, 15 March 2017

OCA: New page: '''Unreleased structure''' The entry 5v2x is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Mar 2017 19:40:42 GMT

New page: '''Unreleased structure''' The entry 5v2x is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5v2x is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]