5d2i - Revision history

OCA at 08:42, 27 September 2023

OCA — Wed, 27 Sep 2023 08:42:38 GMT

←Older revision		Revision as of 08:42, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d2i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D2I FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d2i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D2I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.78Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=5d2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d2i OCA], [https://pdbe.org/5d2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d2i RCSB], [https://www.ebi.ac.uk/pdbsum/5d2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d2i 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=5d2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d2i OCA], [https://pdbe.org/5d2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d2i RCSB], [https://www.ebi.ac.uk/pdbsum/5d2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d2i ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:19, 21 June 2023

OCA — Wed, 21 Jun 2023 10:19:11 GMT

←Older revision		Revision as of 10:19, 21 June 2023
Line 3:		Line 3:
	<StructureSection load='5d2i' size='340' side='right'caption='[[5d2i]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='5d2i' size='340' side='right'caption='[[5d2i]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d2i]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D2I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d2i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D2I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d2f\|5d2f]], [[5d2g\|5d2g]], [[5d2h\|5d2h]], [[5d2j\|5d2j]], [[5d2k\|5d2k]]</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=5d2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d2i OCA], [https://pdbe.org/5d2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d2i RCSB], [https://www.ebi.ac.uk/pdbsum/5d2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d2i ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nahK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-oxo-3-hexenedioate_decarboxylase 2-oxo-3-hexenedioate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.77 4.1.1.77] </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=5d2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d2i OCA], [~~http~~://pdbe.org/5d2i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d2i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d2i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d2i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q1XGK3_PSEPU Q1XGK3_PSEPU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens putidus flugge 1886]]
-	[[Category: 2-oxo-3-hexenedioate decarboxylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Guimaraes, S L~~]]	+	[[Category: Pseudomonas putida]]
-	[[Category: ~~Nagem, R A.P~~]]	+	[[Category: Guimaraes SL]]
-	[[Category: ~~Lyase]]~~	+	[[Category: Nagem RAP]]
-	~~[[Category: Naphthalene degradation~~]]	+

OCA at 06:20, 17 April 2019

OCA — Wed, 17 Apr 2019 06:20:26 GMT

←Older revision		Revision as of 06:20, 17 April 2019
Line 1:		Line 1:

	==4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with calcium and acetate==		==4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with calcium and acetate==
-	<StructureSection load='5d2i' size='340' side='right' caption='[[5d2i]], [[Resolution\|resolution]] 1.78Å' scene=''>	+	<StructureSection load='5d2i' size='340' side='right'caption='[[5d2i]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d2i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d2i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D2I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d2f\|5d2f]], [[5d2g\|5d2g]], [[5d2h\|5d2h]], [[5d2j\|5d2j]], [[5d2k\|5d2k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d2f\|5d2f]], [[5d2g\|5d2g]], [[5d2h\|5d2h]], [[5d2j\|5d2j]], [[5d2k\|5d2k]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nahK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-oxo-3-hexenedioate_decarboxylase 2-oxo-3-hexenedioate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.77 4.1.1.77] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-oxo-3-hexenedioate_decarboxylase 2-oxo-3-hexenedioate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.77 4.1.1.77] </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=5d2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d2i OCA], [http://pdbe.org/5d2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d2i RCSB], [http://www.ebi.ac.uk/pdbsum/5d2i PDBsum]</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=5d2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d2i OCA], [http://pdbe.org/5d2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d2i RCSB], [http://www.ebi.ac.uk/pdbsum/5d2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d2i ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: 2-oxo-3-hexenedioate decarboxylase]]		[[Category: 2-oxo-3-hexenedioate decarboxylase]]
		+	[[Category: Large Structures]]
	[[Category: Guimaraes, S L]]		[[Category: Guimaraes, S L]]
	[[Category: Nagem, R A.P]]		[[Category: Nagem, R A.P]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Naphthalene degradation]]		[[Category: Naphthalene degradation]]

OCA at 03:33, 11 May 2016

OCA — Wed, 11 May 2016 03:33:29 GMT

←Older revision		Revision as of 03:33, 11 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5d2i is ~~ON HOLD until Paper~~ Publication	+	==4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with calcium and acetate==
		+	<StructureSection load='5d2i' size='340' side='right' caption='[[5d2i]], [[Resolution\|resolution]] 1.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5d2i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D2I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d2f\|5d2f]], [[5d2g\|5d2g]], [[5d2h\|5d2h]], [[5d2j\|5d2j]], [[5d2k\|5d2k]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-oxo-3-hexenedioate_decarboxylase 2-oxo-3-hexenedioate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.77 4.1.1.77] </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=5d2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d2i OCA], [http://pdbe.org/5d2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d2i RCSB], [http://www.ebi.ac.uk/pdbsum/5d2i PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg2+ as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent beta-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous beta-keto acid decarboxylase and the first crystal structure of a 4-OD.

-	~~Authors:~~ Guimaraes, ~~S.L.~~, ~~Nagem~~, R.~~A.P~~.	+	Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous beta-Keto Acid.,Guimaraes SL, Coitinho JB, Costa DM, Araujo SS, Whitman CP, Nagem RA Biochemistry. 2016 Apr 27. PMID:27082660<ref>PMID:27082660</ref>

-	~~Description~~: 4-~~oxalocrotonate decarboxylase from Pseudomonas putida G7~~ -~~complexed with calcium and acetate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Nagem, R.A.P]]	+	<div class="pdbe-citations 5d2i" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Guimaraes, S.L~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 2-oxo-3-hexenedioate decarboxylase]]
		+	[[Category: Guimaraes, S L]]
		+	[[Category: Nagem, R A.P]]
		+	[[Category: Lyase]]
		+	[[Category: Naphthalene degradation]]

OCA at 11:09, 2 September 2015

OCA — Wed, 02 Sep 2015 11:09:38 GMT

←Older revision		Revision as of 11:09, 2 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5d2i is ON HOLD	+	The entry 5d2i is ON HOLD until Paper Publication

	Authors: Guimaraes, S.L., Nagem, R.A.P.		Authors: Guimaraes, S.L., Nagem, R.A.P.

OCA: Protected "5d2i" [edit=sysop:move=sysop]

OCA — Wed, 12 Aug 2015 13:45:07 GMT

Protected "5d2i" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:45, 12 August 2015

OCA: New page: '''Unreleased structure''' The entry 5d2i is ON HOLD Authors: Guimaraes, S.L., Nagem, R.A.P. Description: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 -complexed with calc...

OCA — Wed, 12 Aug 2015 13:45:05 GMT

New page: '''Unreleased structure''' The entry 5d2i is ON HOLD Authors: Guimaraes, S.L., Nagem, R.A.P. Description: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 -complexed with calc...

New page

'''Unreleased structure'''

The entry 5d2i is ON HOLD

Authors: Guimaraes, S.L., Nagem, R.A.P.

Description: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 -complexed with calcium and acetate
[[Category: Unreleased Structures]]
[[Category: Nagem, R.A.P]]
[[Category: Guimaraes, S.L]]