5kll - Revision history

OCA at 10:03, 27 September 2023

OCA — Wed, 27 Sep 2023 10:03:19 GMT

←Older revision		Revision as of 10:03, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5kll' size='340' side='right'caption='[[5kll]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='5kll' size='340' side='right'caption='[[5kll]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kll]] is a 4 chain structure with sequence from [https://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=5KLL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KLL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kll]] is a 4 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=5KLL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KLL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6UN:(3~{E},5~{E})-6-OXIDANYL-2-OXIDANYLIDENE-HEXA-3,5-DIENOIC+ACID'>6UN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.17Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5klk\|5klk]], [[5klm\|5klm]], [[5kln\|5kln]], [[5klo\|5klo]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6UN:(3~{E},5~{E})-6-OXIDANYL-2-OXIDANYLIDENE-HEXA-3,5-DIENOIC+ACID'>6UN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaE ([https://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'>[https://proteopedia.org/fgij/fg.htm?mol=5kll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kll OCA], [https://pdbe.org/5kll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kll RCSB], [https://www.ebi.ac.uk/pdbsum/5kll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kll 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=5kll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kll OCA], [https://pdbe.org/5kll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kll RCSB], [https://www.ebi.ac.uk/pdbsum/5kll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kll ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q83V33_PSEFL Q83V33_PSEFL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Davis, I]]	+	[[Category: Pseudomonas fluorescens]]
-	[[Category: Ha, U]]	+	[[Category: Davis I]]
-	[[Category: Liu, A]]	+	[[Category: Ha U]]
-	[[Category: Shin, I]]	+	[[Category: Liu A]]
-	[[Category: Wang, Y]]	+	[[Category: Shin I]]
-	[[Category: Yang, Y]]	+	[[Category: Wang Y]]
-	~~[[Category: 2-aminomuconate 6-semialdehyde dehydrogenase]]~~	+	[[Category: Yang Y]]
-	~~[[Category: Kynurenine pathway]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:22, 26 May 2021

OCA — Wed, 26 May 2021 09:22:40 GMT

←Older revision		Revision as of 09:22, 26 May 2021
Line 3:		Line 3:
	<StructureSection load='5kll' size='340' side='right'caption='[[5kll]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='5kll' size='340' side='right'caption='[[5kll]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kll]] is a 4 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=5KLL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KLL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kll]] is a 4 chain structure with sequence from [https://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=5KLL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KLL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6UN:(3~{E},5~{E})-6-OXIDANYL-2-OXIDANYLIDENE-HEXA-3,5-DIENOIC+ACID'>6UN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6UN:(3~{E},5~{E})-6-OXIDANYL-2-OXIDANYLIDENE-HEXA-3,5-DIENOIC+ACID'>6UN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5klk\|5klk]], [[5klm\|5klm]], [[5kln\|5kln]], [[5klo\|5klo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5klk\|5klk]], [[5klm\|5klm]], [[5kln\|5kln]], [[5klo\|5klo]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaE ([~~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">nbaE ([https://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~~://proteopedia.org/fgij/fg.htm?mol=5kll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kll OCA], [~~http~~://pdbe.org/5kll PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kll RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kll PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kll 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=5kll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kll OCA], [https://pdbe.org/5kll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kll RCSB], [https://www.ebi.ac.uk/pdbsum/5kll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kll ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aldehyde dehydrogenase typically performs oxidation of aldehydes to their corresponding carboxylic acid while reducing NAD(P)(+) to NAD(P)H via covalent catalysis mediated by an active-site cysteine residue. One member of this superfamily, the enzyme 2-aminomuconate-6-semialdehyde dehydrogenase (AMSDH), is a component of the kynurenine pathway, which catabolizes tryptophan in mammals and certain bacteria. AMSDH catalyzes the NAD(+)-dependent oxidation of 2-aminomuconate semialdehyde to 2-aminomuconate. We recently determined the first crystal structure of AMSDH and several catalytic cycle intermediates. A conserved asparagine in the oxyanion hole, Asn-169, is found to be H-bonded to substrate-derived intermediates in the active site of AMSDH during catalysis, including both the covalently bound thiohemiacetal and thioacyl intermediates. To better interrogate the significance of the hydrogen bond provided by Asn-169 to the reaction mechanism of AMSDH, we created Ala, Ser, Asp, and Gln mutants and studied them using biochemical, kinetic, crystallographic, and computational studies. The in crystallo chemical reaction of the primary substrate with the co-crystalized complex of the N169D mutant and NAD(+) led to the successful trapping of a new catalytic intermediate that was not previously seen. The structural and computational data are consistent with a substrate imine/enol tautomer intermediate being formed prior to the formation of the covalent bond between the substrate and the active-site cysteine. Thus, AMSDH surprisingly includes an isomerization process within its known catalytic mechanism. These data establish a hidden intrinsic isomerization activity of the dehydrogenase and allow us to propose a pitcher-catcher type of catalytic mechanism for the isomerization.
		+
		+	A Pitcher-and-Catcher Mechanism Drives Endogenous Substrate Isomerization by a Dehydrogenase in Kynurenine Metabolism.,Yang Y, Davis I, Ha U, Wang Y, Shin I, Liu A J Biol Chem. 2016 Dec 16;291(51):26252-26261. doi: 10.1074/jbc.M116.759712. Epub , 2016 Nov 3. PMID:27810899<ref>PMID:27810899</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kll" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:28, 8 July 2020

OCA — Wed, 08 Jul 2020 15:28:15 GMT

←Older revision		Revision as of 15:28, 8 July 2020
Line 1:		Line 1:

	==Crystal structure of 2-hydroxymuconate-6-semialdehyde derived tautomeric intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169D==		==Crystal structure of 2-hydroxymuconate-6-semialdehyde derived tautomeric intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169D==
-	<StructureSection load='5kll' size='340' side='right' caption='[[5kll]], [[Resolution\|resolution]] 2.17Å' scene=''>	+	<StructureSection load='5kll' size='340' side='right'caption='[[5kll]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kll]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KLL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KLL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kll]] is a 4 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=5KLL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KLL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6UN:(3~{E},5~{E})-6-OXIDANYL-2-OXIDANYLIDENE-HEXA-3,5-DIENOIC+ACID'>6UN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6UN:(3~{E},5~{E})-6-OXIDANYL-2-OXIDANYLIDENE-HEXA-3,5-DIENOIC+ACID'>6UN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5klk\|5klk]], [[5klm\|5klm]], [[5kln\|5kln]], [[5klo\|5klo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5klk\|5klk]], [[5klm\|5klm]], [[5kln\|5kln]], [[5klo\|5klo]]</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=5kll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kll OCA], [http://pdbe.org/5kll PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kll RCSB], [http://www.ebi.ac.uk/pdbsum/5kll PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kll ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaE ([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://proteopedia.org/fgij/fg.htm?mol=5kll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kll OCA], [http://pdbe.org/5kll PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kll RCSB], [http://www.ebi.ac.uk/pdbsum/5kll PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kll ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Davis, I]]		[[Category: Davis, I]]
	[[Category: Ha, U]]		[[Category: Ha, U]]

OCA at 19:53, 9 December 2016

OCA — Fri, 09 Dec 2016 19:53:09 GMT

←Older revision		Revision as of 19:53, 9 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5kll is ON HOLD until Jun 24 2018~~	+	==Crystal structure of 2-hydroxymuconate-6-semialdehyde derived tautomeric intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169D==
-		+	<StructureSection load='5kll' size='340' side='right' caption='[[5kll]], [[Resolution\|resolution]] 2.17Å' scene=''>
-	~~Authors: Yang, Y., Davis, I., Ha, U., Wang, Y., Shin, I. , Liu, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kll]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KLL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KLL FirstGlance]. <br>
-	~~Description:~~ Crystal structure of 2-hydroxymuconate-6-semialdehyde derived tautomeric intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169D	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6UN:(3~{E},5~{E})-6-OXIDANYL-2-OXIDANYLIDENE-HEXA-3,5-DIENOIC+ACID'>6UN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5klk\|5klk]], [[5klm\|5klm]], [[5kln\|5kln]], [[5klo\|5klo]]</td></tr>
-	[[~~Category~~: ~~Yang~~, Y]]	+	<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=5kll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kll OCA], [http://pdbe.org/5kll PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kll RCSB], [http://www.ebi.ac.uk/pdbsum/5kll PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kll ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Wang~~, Y]]	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Davis, I]]		[[Category: Davis, I]]
	[[Category: Ha, U]]		[[Category: Ha, U]]
-	[[Category: Shin, I. , ~~Liu~~, A]]	+	[[Category: Liu, A]]
		+	[[Category: Shin, I]]
		+	[[Category: Wang, Y]]
		+	[[Category: Yang, Y]]
		+	[[Category: 2-aminomuconate 6-semialdehyde dehydrogenase]]
		+	[[Category: Kynurenine pathway]]
		+	[[Category: Oxidoreductase]]

OCA at 15:07, 26 October 2016

OCA — Wed, 26 Oct 2016 15:07:18 GMT

←Older revision		Revision as of 15:07, 26 October 2016
Line 3:		Line 3:
	The entry 5kll is ON HOLD until Jun 24 2018		The entry 5kll is ON HOLD until Jun 24 2018

-	Authors: Yang, Y., Davis, I., Ha, U., Wang, Y., ~~Iwaki~~, ~~H., Hasegawa, Y~~., Liu, A.	+	Authors: Yang, Y., Davis, I., Ha, U., Wang, Y., Shin, I. , Liu, A.

	Description: Crystal structure of 2-hydroxymuconate-6-semialdehyde derived tautomeric intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169D		Description: Crystal structure of 2-hydroxymuconate-6-semialdehyde derived tautomeric intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169D
Line 11:		Line 11:
	[[Category: Davis, I]]		[[Category: Davis, I]]
	[[Category: Ha, U]]		[[Category: Ha, U]]
-	[[Category: ~~Hasegawa~~, ~~Y]]~~	+	[[Category: Shin, I. , Liu, A]]
-	~~[[Category:~~ Liu, A]]	+
-	~~[[Category: Iwaki, H~~]]	+

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

OCA — Wed, 13 Jul 2016 00:31:57 GMT

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

←Older revision

Revision as of 00:31, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kll is ON HOLD until Jun 24 2018 Authors: Yang, Y., Davis, I., Ha, U., Wang, Y., Iwaki, H., Hasegawa, Y., Liu, A. Description: Crystal structure o...

OCA — Wed, 13 Jul 2016 00:31:56 GMT

New page: '''Unreleased structure''' The entry 5kll is ON HOLD until Jun 24 2018 Authors: Yang, Y., Davis, I., Ha, U., Wang, Y., Iwaki, H., Hasegawa, Y., Liu, A. Description: Crystal structure o...

New page

'''Unreleased structure'''

The entry 5kll is ON HOLD until Jun 24 2018

Authors: Yang, Y., Davis, I., Ha, U., Wang, Y., Iwaki, H., Hasegawa, Y., Liu, A.

Description: Crystal structure of 2-hydroxymuconate-6-semialdehyde derived tautomeric intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169D
[[Category: Unreleased Structures]]
[[Category: Yang, Y]]
[[Category: Wang, Y]]
[[Category: Davis, I]]
[[Category: Ha, U]]
[[Category: Hasegawa, Y]]
[[Category: Liu, A]]
[[Category: Iwaki, H]]