6mgs - Revision history

OCA at 06:31, 11 October 2023

OCA — Wed, 11 Oct 2023 06:31:31 GMT

←Older revision		Revision as of 06:31, 11 October 2023
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	<StructureSection load='6mgs' size='340' side='right'caption='[[6mgs]], [[Resolution\|resolution]] 3.13Å' scene=''>		<StructureSection load='6mgs' size='340' side='right'caption='[[6mgs]], [[Resolution\|resolution]] 3.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mgs]] is a 3 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=6MGS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MGS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mgs]] is a 3 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=6MGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MGS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CO:COBALT+(II)+ION'>CO</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]] 3.131Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></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=6mgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgs OCA], [~~http~~://pdbe.org/6mgs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mgs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mgs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgs 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=6mgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgs OCA], [https://pdbe.org/6mgs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mgs RCSB], [https://www.ebi.ac.uk/pdbsum/6mgs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgs 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Davis, I]]	+	[[Category: Pseudomonas fluorescens]]
-	[[Category: Liu, A]]	+	[[Category: Davis I]]
-	[[Category: Matsui, T]]	+	[[Category: Liu A]]
-	[[Category: Rubalcava, I]]	+	[[Category: Matsui T]]
-	[[Category: Yang, Y]]	+	[[Category: Rubalcava I]]
-	~~[[Category: Decarboxylase]]~~	+	[[Category: Yang Y]]
-	~~[[Category: Holo structure]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 06:17, 7 August 2019

OCA — Wed, 07 Aug 2019 06:17:57 GMT

←Older revision		Revision as of 06:17, 7 August 2019
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	<StructureSection load='6mgs' size='340' side='right'caption='[[6mgs]], [[Resolution\|resolution]] 3.13Å' scene=''>		<StructureSection load='6mgs' size='340' side='right'caption='[[6mgs]], [[Resolution\|resolution]] 3.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mgs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MGS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mgs]] is a 3 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=6MGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MGS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></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=6mgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgs OCA], [http://pdbe.org/6mgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mgs RCSB], [http://www.ebi.ac.uk/pdbsum/6mgs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgs 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=6mgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgs OCA], [http://pdbe.org/6mgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mgs RCSB], [http://www.ebi.ac.uk/pdbsum/6mgs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgs ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Davis, I]]		[[Category: Davis, I]]

OCA at 07:30, 26 June 2019

OCA — Wed, 26 Jun 2019 07:30:12 GMT

←Older revision		Revision as of 07:30, 26 June 2019
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	<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=6mgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgs OCA], [http://pdbe.org/6mgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mgs RCSB], [http://www.ebi.ac.uk/pdbsum/6mgs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgs 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=6mgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgs OCA], [http://pdbe.org/6mgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mgs RCSB], [http://www.ebi.ac.uk/pdbsum/6mgs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgs ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	alpha-Amino-beta-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) plays an important role in L-tryptophan degradation via the kynurenine pathway. ACMSD forms a homodimer and is functionally inactive as a monomer because its catalytic assembly requires an arginine residue from a neighboring subunit. However, how the oligomeric state and self-association of ACMSD are controlled in solution remains unexplored. Here, we demonstrate that ACMSD from Pseudomonas fluorescens can self-assemble into homodimer, tetramer, and higher-order structures. Using size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS) analysis, we investigated the ACMSD tetramer structure, and fitting the SAXS data with X-ray crystal structures of the monomeric component; we could generate a pseudo-atomic structure of the tetramer. This analysis revealed a tetramer model of ACMSD as a head-on dimer of dimers. We observed that the tetramer is catalytically more active than the dimer and is in equilibrium with the monomer and dimer. Substituting a critical residue of the dimer-dimer interface, His-110, altered the tetramer dissociation profile by increasing the higher-order oligomer portion in solution without changing the X-ray crystal structure. ACMSD self-association was affected by pH, ionic strength, and other electrostatic interactions. Alignment of ACMSD sequences revealed that His-110 is highly conserved in a few bacteria that utilize nitrobenzoic acid as a sole source of carbon and energy, suggesting a dedicated functional role of ACMSD's self-assembly into the tetrameric and higher-order structures. These results indicate that the dynamic oligomerization status potentially regulates ACMSD activity and that SEC-SAXS coupled with X-ray crystallography is a powerful tool for studying protein self-association.
		+
		+	Quaternary structure of alpha-amino-beta-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) controls its activity.,Yang Y, Davis I, Matsui T, Rubalcava I, Liu A J Biol Chem. 2019 Jun 12. pii: RA119.009035. doi: 10.1074/jbc.RA119.009035. PMID:31189654<ref>PMID:31189654</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6mgs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:59, 19 June 2019

OCA — Wed, 19 Jun 2019 05:59:25 GMT

←Older revision		Revision as of 05:59, 19 June 2019
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-	'''Unreleased structure'''

-	~~The entry 6mgs is ON HOLD until Paper Publication~~	+	==Crystal structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase with Space Group of C2221==
-		+	<StructureSection load='6mgs' size='340' side='right'caption='[[6mgs]], [[Resolution\|resolution]] 3.13Å' scene=''>
-	~~Authors: Yang, Y., Davis, I., Matsui, T., Rubalcava, I., Liu, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6mgs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MGS FirstGlance]. <br>
-	~~Description:~~ Crystal structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase with Space Group of C2221	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6mgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgs OCA], [http://pdbe.org/6mgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mgs RCSB], [http://www.ebi.ac.uk/pdbsum/6mgs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgs ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Matsui~~, T]]	+	</table>
-	[[Category: ~~Yang, Y~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Davis, I]]		[[Category: Davis, I]]
	[[Category: Liu, A]]		[[Category: Liu, A]]
		+	[[Category: Matsui, T]]
	[[Category: Rubalcava, I]]		[[Category: Rubalcava, I]]
		+	[[Category: Yang, Y]]
		+	[[Category: Decarboxylase]]
		+	[[Category: Holo structure]]
		+	[[Category: Lyase]]

OCA at 06:26, 10 October 2018

OCA — Wed, 10 Oct 2018 06:26:47 GMT

←Older revision		Revision as of 06:26, 10 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Yang, Y., Davis, I., Matsui, T., Rubalcava, I., Liu, A.		Authors: Yang, Y., Davis, I., Matsui, T., Rubalcava, I., Liu, A.

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

OCA — Wed, 26 Sep 2018 06:29:59 GMT

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

←Older revision

Revision as of 06:29, 26 September 2018

OCA: New page: '''Unreleased structure''' The entry 6mgs is ON HOLD Authors: Yang, Y., Davis, I., Matsui, T., Rubalcava, I., Liu, A. Description: Crystal structure of alpha-Amino-beta-Carboxymuconate...

OCA — Wed, 26 Sep 2018 06:29:58 GMT

New page: '''Unreleased structure''' The entry 6mgs is ON HOLD Authors: Yang, Y., Davis, I., Matsui, T., Rubalcava, I., Liu, A. Description: Crystal structure of alpha-Amino-beta-Carboxymuconate...

New page

'''Unreleased structure'''

The entry 6mgs is ON HOLD

Authors: Yang, Y., Davis, I., Matsui, T., Rubalcava, I., Liu, A.

Description: Crystal structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase with Space Group of C2221
[[Category: Unreleased Structures]]
[[Category: Matsui, T]]
[[Category: Yang, Y]]
[[Category: Davis, I]]
[[Category: Liu, A]]
[[Category: Rubalcava, I]]