4ifo - Revision history

OCA at 15:21, 20 September 2023

2023-09-20T15:21:27Z

←Older revision		Revision as of 15:21, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ifo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IFO FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ifo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IFO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4ifo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ifo OCA], [https://pdbe.org/4ifo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ifo RCSB], [https://www.ebi.ac.uk/pdbsum/4ifo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ifo 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=4ifo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ifo OCA], [https://pdbe.org/4ifo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ifo RCSB], [https://www.ebi.ac.uk/pdbsum/4ifo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ifo ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:09, 9 November 2022

2022-11-09T09:09:16Z

←Older revision		Revision as of 09:09, 9 November 2022
Line 1:		Line 1:

	==2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens==		==2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens==
-	<StructureSection load='4ifo' size='340' side='right' caption='[[4ifo]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4ifo' size='340' side='right'caption='[[4ifo]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ifo]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus~~ fluorescens ~~liquefaciens" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ifo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IFO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ifk\|4ifk]], [[4ifr\|4ifr]], [[4ig2\|4ig2]], [[4ih3\|4ih3]]</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=4ifo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ifo OCA], [https://pdbe.org/4ifo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ifo RCSB], [https://www.ebi.ac.uk/pdbsum/4ifo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ifo ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=4ifo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ifo OCA], [~~http~~://pdbe.org/4ifo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ifo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ifo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ifo ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q83V25_PSEFL Q83V25_PSEFL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ fluorescens ~~liquefaciens flugge 1886~~]]	+	[[Category: Large Structures]]
-	[[Category: Chen, L]]	+	[[Category: Pseudomonas fluorescens]]
-	[[Category: Davis, I]]	+	[[Category: Chen L]]
-	[[Category: Huo, L]]	+	[[Category: Davis I]]
-	[[Category: Liu, A]]	+	[[Category: Huo L]]
-	~~[[Category: Decarboxylation]]~~	+	[[Category: Liu A]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 10:05, 11 August 2016

2016-08-11T10:05:03Z

←Older revision		Revision as of 10:05, 11 August 2016
Line 1:		Line 1:
		+
	==2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens==		==2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens==
	<StructureSection load='4ifo' size='340' side='right' caption='[[4ifo]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4ifo' size='340' side='right' caption='[[4ifo]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ifk\|4ifk]], [[4ifr\|4ifr]], [[4ig2\|4ig2]], [[4ih3\|4ih3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ifk\|4ifk]], [[4ifr\|4ifr]], [[4ig2\|4ig2]], [[4ih3\|4ih3]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=4ifo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ifo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ifo RCSB], [http://www.ebi.ac.uk/pdbsum/4ifo 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=4ifo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ifo OCA], [http://pdbe.org/4ifo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ifo RCSB], [http://www.ebi.ac.uk/pdbsum/4ifo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ifo ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4ifo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:50, 4 January 2015

2015-01-04T13:50:54Z

←Older revision		Revision as of 13:50, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4ifo\| PDB=4ifo \| SCENE= }}~~	+	==2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens==
-	===2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens===	+	<StructureSection load='4ifo' size='340' side='right' caption='[[4ifo]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24019523}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ifo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IFO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ifk\|4ifk]], [[4ifr\|4ifr]], [[4ig2\|4ig2]], [[4ih3\|4ih3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=4ifo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ifo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ifo RCSB], [http://www.ebi.ac.uk/pdbsum/4ifo PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Although the crystal structure of alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase from Pseudomonas fluorescens was solved as a dimer, this enzyme is a mixture of monomer, dimer, and higher order structures in solution. In this work, we found that the dimeric state, not the monomeric state, is the functionally active form. Two conserved arginine residues are present in the active site: Arg-51 and an intruding Arg-239* from the neighboring subunit. In this study, they were each mutated to alanine and lysine, and all four mutants were catalytically inactive. The mutants were also incapable of accommodating pyridine-2,6-dicarboxylic acid, a competitive inhibitor of the native enzyme, suggesting that the two Arg residues are involved in substrate binding. It was also observed that the decarboxylase activity was partially recovered in a heterodimer hybridization experiment when inactive R51(A/K) and R239(A/K) mutants were mixed together. Of the 20 crystal structures obtained from mixing inactive R51A and R239A homodimers that diffracted to a resolution lower than 3.00 A, two structures are clearly R51A/R239A heterodimers and belong to the C2 space group. They were refined to 1.80 and 2.00 A resolutions, respectively. Four of the remaining crystals are apparently single mutants and belong to the P42212 space group. In the heterodimer structures, one active site is shown to contain dual mutation of Ala-51 and Ala-239, whereas the other contains the native Arg-51 and Arg-239 residues, identical to the wild-type structure. Thus, these observations provide the foundation for a molecular mechanism by which the oligomerization state of alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase could regulate the enzyme activity.

-	~~==About this Structure==~~	+	The power of two: arginine 51 and arginine 239* from a neighboring subunit are essential for catalysis in alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase.,Huo L, Davis I, Chen L, Liu A J Biol Chem. 2013 Oct 25;288(43):30862-71. doi: 10.1074/jbc.M113.496869. Epub, 2013 Sep 9. PMID:24019523<ref>PMID:24019523</ref>
-	~~[[4ifo]] is a 2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4IFO OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024019523</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]		[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
-	[[Category: Chen, L.]]	+	[[Category: Chen, L]]
-	[[Category: Davis, I.]]	+	[[Category: Davis, I]]
-	[[Category: Huo, L.]]	+	[[Category: Huo, L]]
-	[[Category: Liu, A.]]	+	[[Category: Liu, A]]
	[[Category: Decarboxylation]]		[[Category: Decarboxylation]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 08:36, 25 December 2013

2013-12-25T08:36:15Z

←Older revision		Revision as of 08:36, 25 December 2013
Line 1:		Line 1:
	{{STRUCTURE_4ifo\| PDB=4ifo \| SCENE= }}		{{STRUCTURE_4ifo\| PDB=4ifo \| SCENE= }}
	===2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens===		===2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens===
		+	{{ABSTRACT_PUBMED_24019523}}

	==About this Structure==		==About this Structure==
-	[[4ifo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_mikatae Saccharomyces mikatae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFO OCA].	+	[[4ifo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFO OCA].
-	[[Category: ~~Saccharomyces mikatae~~]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:024019523</ref><references group="xtra"/><references/>
		+	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Chen, L.]]		[[Category: Chen, L.]]
	[[Category: Davis, I.]]		[[Category: Davis, I.]]

OCA at 04:19, 20 September 2013

2013-09-20T04:19:50Z

←Older revision		Revision as of 04:19, 20 September 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4ifo\| PDB=4ifo \| SCENE= }}
		+	===2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens===

-	~~The entry~~ 4ifo is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4ifo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_mikatae Saccharomyces mikatae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IFO OCA].
-	~~Authors~~: ~~Huo~~, L., Davis, I.~~, Chen~~, L., Liu, A.	+	[[Category: Saccharomyces mikatae]]
-		+	[[Category: Chen, L.]]
-	~~Description~~: ~~2.50 Angstroms X-ray crystal structure of R51A 2-amino~~-~~3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens~~	+	[[Category: Davis, I.]]
		+	[[Category: Huo, L.]]
		+	[[Category: Liu, A.]]
		+	[[Category: Decarboxylation]]
		+	[[Category: Lyase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Tim barrel]]

OCA at 10:04, 13 February 2013

2013-02-13T10:04:14Z

←Older revision		Revision as of 10:04, 13 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ifo is ON HOLD	+	The entry 4ifo is ON HOLD until Paper Publication

	Authors: Huo, L., Davis, I., Chen, L., Liu, A.		Authors: Huo, L., Davis, I., Chen, L., Liu, A.

	Description: 2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens		Description: 2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens

OCA: Protected "4ifo" [edit=sysop:move=sysop]

2013-01-02T08:56:44Z

Protected "4ifo" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:56, 2 January 2013

OCA: New page: '''Unreleased structure''' The entry 4ifo is ON HOLD Authors: Huo, L., Davis, I., Chen, L., Liu, A. Description: 2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconat...

2013-01-02T08:56:43Z

New page: '''Unreleased structure''' The entry 4ifo is ON HOLD Authors: Huo, L., Davis, I., Chen, L., Liu, A. Description: 2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconat...

New page

'''Unreleased structure'''

The entry 4ifo is ON HOLD

Authors: Huo, L., Davis, I., Chen, L., Liu, A.

Description: 2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens