4i9b - Revision history

OCA at 14:13, 8 November 2023

OCA — Wed, 08 Nov 2023 14:13:07 GMT

←Older revision		Revision as of 14:13, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4i9b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I9B FirstGlance]. <br>		<table><tr><td colspan='2'>[[4i9b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I9B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1KA:(2-HYDROXYETHOXY)ACETALDEHYDE'>1KA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1KA:(2-HYDROXYETHOXY)ACETALDEHYDE'>1KA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=4i9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i9b OCA], [https://pdbe.org/4i9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i9b RCSB], [https://www.ebi.ac.uk/pdbsum/4i9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i9b 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=4i9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i9b OCA], [https://pdbe.org/4i9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i9b RCSB], [https://www.ebi.ac.uk/pdbsum/4i9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i9b ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:50, 9 November 2022

OCA — Wed, 09 Nov 2022 08:50:03 GMT

←Older revision		Revision as of 08:50, 9 November 2022
Line 1:		Line 1:

	==Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate==		==Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate==
-	<StructureSection load='4i9b' size='340' side='right' caption='[[4i9b]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4i9b' size='340' side='right'caption='[[4i9b]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i9b]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lycopersicon_esculentum Lycopersicon esculentum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I9B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i9b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I9B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1KA:(2-HYDROXYETHOXY)ACETALDEHYDE'>1KA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1KA:(2-HYDROXYETHOXY)ACETALDEHYDE'>1KA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iwj\|3iwj]], [[3iwk\|3iwk]], [[4i8p\|4i8p]], [[4i8q\|4i8q]]</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=4i9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i9b OCA], [https://pdbe.org/4i9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i9b RCSB], [https://www.ebi.ac.uk/pdbsum/4i9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i9b ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Solyc06g071290.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=4i9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i9b OCA], [~~http~~://pdbe.org/4i9b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i9b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i9b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i9b ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AADH1_SOLLC AADH1_SOLLC] Dehydrogenase that catalyzes the oxidation of several aminoaldehydes (PubMed:23408433). Metabolizes and detoxifies aldehyde products of polyamine degradation to non-toxic amino acids (Probable). Catalyzes the oxidation of 4-aminobutanal and 3-aminopropanal to 4-aminobutanoate and beta-alanine, respectively (PubMed:23408433). Catalyzes the oxidation of 4-(trimethylamino)butanal and 4-guanidinobutanal to 4-trimethylammoniobutanoate and 4-guanidinobutanoate, respectively (PubMed:23408433). Catalyzes with low efficiency the oxidation of betaine aldehyde to glycine betaine (PubMed:23408433).<ref>PMID:23408433</ref>
	<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: ~~Lycopersicon esculentum~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kopecny, D~~]]	+	[[Category: Solanum lycopersicum]]
-	[[Category: ~~Morera, S~~]]	+	[[Category: Kopecny D]]
-	[[Category: ~~Vigouroux, A~~]]	+	[[Category: Morera S]]
-	[[Category: ~~Aldh10 family fold]]~~	+	[[Category: Vigouroux A]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:53, 4 August 2016

OCA — Thu, 04 Aug 2016 08:53:18 GMT

←Older revision		Revision as of 08:53, 4 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_4i9b\| PDB=4i9b \| SCENE= }}
-	===Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate===
-	{{ABSTRACT_PUBMED_23408433}}

-	==~~About this~~ Structure==	+	==Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate==
-	[[4i9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9B OCA].	+	<StructureSection load='4i9b' size='340' side='right' caption='[[4i9b]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4i9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I9B FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1KA:(2-HYDROXYETHOXY)ACETALDEHYDE'>1KA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iwj\|3iwj]], [[3iwk\|3iwk]], [[4i8p\|4i8p]], [[4i8q\|4i8q]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Solyc06g071290.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=4i9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i9b OCA], [http://pdbe.org/4i9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i9b RCSB], [http://www.ebi.ac.uk/pdbsum/4i9b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i9b ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plant ALDH10 family members are aminoaldehyde dehydrogenases (AMADHs), which oxidize omega-aminoaldehydes to the corresponding acids. They have been linked to polyamine catabolism, osmoprotection, secondary metabolism (fragrance), and carnitine biosynthesis. Plants commonly contain two AMADH isoenzymes. We previously studied the substrate specificity of two AMADH isoforms from peas (PsAMADHs). Here, two isoenzymes from tomato (Solanum lycopersicum), SlAMADHs, and three AMADHs from maize (Zea mays), ZmAMADHs, were kinetically investigated to obtain further clues to the catalytic mechanism and the substrate specificity. We also solved the high resolution crystal structures of SlAMADH1 and ZmAMADH1a because these enzymes stand out from the others regarding their activity. From the structural and kinetic analysis, we can state that five residues at positions 163, 288, 289, 444, and 454 (PsAMADHs numbering) can, directly or not, significantly modulate AMADH substrate specificity. In the SlAMADH1 structure, a PEG aldehyde derived from the precipitant forms a thiohemiacetal intermediate, never observed so far. Its absence in the SlAMADH1-E260A structure suggests that Glu-260 can activate the catalytic cysteine as a nucleophile. We show that the five AMADHs studied here are capable of oxidizing 3-dimethylsulfoniopropionaldehyde to the cryo- and osmoprotectant 3-dimethylsulfoniopropionate. For the first time, we also show that 3-acetamidopropionaldehyde, the third aminoaldehyde besides 3-aminopropionaldehyde and 4-aminobutyraldehyde, is generally oxidized by AMADHs, meaning that these enzymes are unique in metabolizing and detoxifying aldehyde products of polyamine degradation to nontoxic amino acids. Finally, gene expression profiles in maize indicate that AMADHs might be important for controlling omega-aminoaldehyde levels during early stages of the seed development.

-	~~==Reference==~~	+	Plant ALDH10 family: identifying critical residues for substrate specificity and trapping a thiohemiacetal intermediate.,Kopecny D, Koncitikova R, Tylichova M, Vigouroux A, Moskalikova H, Soural M, Sebela M, Morera S J Biol Chem. 2013 Mar 29;288(13):9491-507. doi: 10.1074/jbc.M112.443952. Epub, 2013 Feb 13. PMID:23408433<ref>PMID:23408433</ref>
-	<ref ~~group="xtra"~~>PMID:~~023408433~~</ref><~~references group~~="~~xtra~~"/><references/>	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4i9b" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Lycopersicon esculentum]]		[[Category: Lycopersicon esculentum]]
-	[[Category: Kopecny, D.]]	+	[[Category: Kopecny, D]]
-	[[Category: Morera, S.]]	+	[[Category: Morera, S]]
-	[[Category: Vigouroux, A.]]	+	[[Category: Vigouroux, A]]
	[[Category: Aldh10 family fold]]		[[Category: Aldh10 family fold]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 10:43, 1 January 2014

OCA — Wed, 01 Jan 2014 10:43:19 GMT

←Older revision		Revision as of 10:43, 1 January 2014
Line 1:		Line 1:
-	[[Image:4i9b.jpg\|left\|200px]]
-
	{{STRUCTURE_4i9b\| PDB=4i9b \| SCENE= }}		{{STRUCTURE_4i9b\| PDB=4i9b \| SCENE= }}
-
	===Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate===		===Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate===
		+	{{ABSTRACT_PUBMED_23408433}}

		+	==About this Structure==
		+	[[4i9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9B OCA].

-	==~~About this Structure~~==	+	==Reference==
-	~~[[4i9b]] is a 2 chain structure with sequence from [http~~://~~en.wikipedia.org~~/~~wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9B OCA].~~	+	<ref group="xtra">PMID:023408433</ref><references group="xtra"/><references/>
-	[[Category: ~~Solanum lycopersicum~~]]	+	[[Category: Lycopersicon esculentum]]
	[[Category: Kopecny, D.]]		[[Category: Kopecny, D.]]
	[[Category: Morera, S.]]		[[Category: Morera, S.]]

OCA at 14:00, 20 February 2013

OCA — Wed, 20 Feb 2013 14:00:24 GMT

←Older revision		Revision as of 14:00, 20 February 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4i9b.jpg\|left\|200px]]

-	~~The entry~~ 4i9b ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4i9b\| PDB=4i9b \| SCENE= }}

-	~~Authors: Morera, S., Vigouroux, A., Kopecny, D.~~	+	===Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate===

-	~~Description:~~ Structure ~~of aminoaldehyde dehydrogenase 1~~ from Solanum ~~lycopersium (SlAMADH1) with a thiohemiacetal intermediate~~	+
		+	==About this Structure==
		+	[[4i9b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I9B OCA].
		+	[[Category: Solanum lycopersicum]]
		+	[[Category: Kopecny, D.]]
		+	[[Category: Morera, S.]]
		+	[[Category: Vigouroux, A.]]
		+	[[Category: Aldh10 family fold]]
		+	[[Category: Oxidoreductase]]

OCA at 11:59, 30 January 2013

OCA — Wed, 30 Jan 2013 11:59:18 GMT

←Older revision		Revision as of 11:59, 30 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4i9b is ON HOLD until ~~sometime in the future~~	+	The entry 4i9b is ON HOLD until Paper Publication

	Authors: Morera, S., Vigouroux, A., Kopecny, D.		Authors: Morera, S., Vigouroux, A., Kopecny, D.

	Description: Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate		Description: Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate

OCA at 08:22, 16 January 2013

OCA — Wed, 16 Jan 2013 08:22:26 GMT

←Older revision		Revision as of 08:22, 16 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4i9b is ON HOLD	+	The entry 4i9b is ON HOLD until sometime in the future

	Authors: Morera, S., Vigouroux, A., Kopecny, D.		Authors: Morera, S., Vigouroux, A., Kopecny, D.

	Description: Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate		Description: Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate

OCA at 08:54, 2 January 2013

OCA — Wed, 02 Jan 2013 08:54:12 GMT

←Older revision		Revision as of 08:54, 2 January 2013
Line 3:		Line 3:
	The entry 4i9b is ON HOLD		The entry 4i9b is ON HOLD

-	Authors: Morera, S, Vigouroux, A, Kopecny, D	+	Authors: Morera, S., Vigouroux, A., Kopecny, D.

	Description: Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate		Description: Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate

OCA: Protected "4i9b" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2012 20:51:28 GMT

Protected "4i9b" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:51, 12 December 2012

OCA: New page: '''Unreleased structure''' The entry 4i9b is ON HOLD Authors: Morera, S, Vigouroux, A, Kopecny, D Description: Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAM...

OCA — Wed, 12 Dec 2012 20:51:27 GMT

New page: '''Unreleased structure''' The entry 4i9b is ON HOLD Authors: Morera, S, Vigouroux, A, Kopecny, D Description: Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAM...

New page

'''Unreleased structure'''

The entry 4i9b is ON HOLD

Authors: Morera, S, Vigouroux, A, Kopecny, D

Description: Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate