The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+/enzyme interactions

Langendorf, C.G.; Key, T.L.; Fenalti, G.; Kan, W.T.; Buckle, A.M.; Caradoc-Davies, T.; Tuck, K.L.; Law, R.H.; Whisstock, J.C.; PLoS One 5, e9280 (2010)

Data extracted from this reference:

Application

Application	Commentary	Organism
medicine	analysis of Escherichia coli SSADH structure with respect to human disease-linked mutations	Escherichia coli K-12

Cloned(Commentary)

Commentary	Organism
-	Escherichia coli K-12
expressed in Escherichia coli BL21(DE3) cells	Escherichia coli

Crystallization (Commentary)

Crystallization	Organism
comparison to human enzyme, analysis of NADP+ binding site. Enzyme is a homotetramer with the 4 monomers related by a non-crystallographic 222 symmetry. The conserved catalytic site residues and active site residues correspond to C288 and E254 as well as R164, R282 and S445, respectively	Escherichia coli K-12
in complex with NADP+, hanging drop vapour diffusion method, using 0.2 M ammonium tartrate, 26-31% polyethylene glycol 3350, 10 mM beta-mercaptoethanol and 0.1 M Tris (pH 7.2-7.5)	Escherichia coli

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Commentary	Organism	Structure
0.01694	-	Succinate semialdehyde	in 100 mM sodium phosphate buffer, pH 8.0, 30°C	Escherichia coli
0.01694	-	Succinate semialdehyde	pH 8.0, 30°C	Escherichia coli K-12

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Commentary (Nat. Sub.)	Natural Products	Commentary (Nat. Pro.)	Organism (Nat. Pro.)	Reversibility
succinate semialdehyde + NAD+ + H2O	Escherichia coli	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	succinate + NADH + H+	-	-	?
succinate semialdehyde + NADP+ + H2O	Escherichia coli	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	succinate + NADPH + H+	-	-	?

Organism

Organism	Primary Accession No. (UniProt)	Commentary	Textmining
Escherichia coli	P25526	-	-
Escherichia coli K-12	P25526	-	-
Escherichia coli MC1061	P25526	-	-

Purification (Commentary)

Commentary	Organism
nickel chelating Sepharose column chromatography and S200 16/60 gel filtration	Escherichia coli
recombinant enzyme	Escherichia coli K-12

Substrates and Products (Substrate)

Substrates	Commentary Substrates	Literature (Substrates)	Organism	Products	Commentary (Products)	Literature (Products)	Organism (Products)	Reversibility
succinate semialdehyde + NAD+ + H2O	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	710394	Escherichia coli	succinate + NADH + H+	-	-	-	?
succinate semialdehyde + NADP+ + H2O	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	710394	Escherichia coli	succinate + NADPH + H+	-	-	-	?
succinate semialdehyde + NADP+ + H2O	-	710394	Escherichia coli K-12	succinate + NADPH + 2 H+	-	-	-	?

Subunits

Subunits	Commentary	Organism
tetramer	crystallographic data	Escherichia coli K-12
tetramer	x-ray crystallography	Escherichia coli

Cofactor

Cofactor	Commentary	Organism	Structure
additional information	no cofactor: NAD+	Escherichia coli K-12	-
NAD+	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	Escherichia coli
NADP+	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	Escherichia coli
NADP+	electron density analysis of binding site. The enzyme activity measured in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	Escherichia coli K-12

Application (protein specific)

Application	Commentary	Organism
medicine	analysis of Escherichia coli SSADH structure with respect to human disease-linked mutations	Escherichia coli K-12

Cloned(Commentary) (protein specific)

Commentary	Organism
-	Escherichia coli K-12
expressed in Escherichia coli BL21(DE3) cells	Escherichia coli

Cofactor (protein specific)

Cofactor	Commentary	Organism	Structure
additional information	no cofactor: NAD+	Escherichia coli K-12	-
NAD+	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	Escherichia coli
NADP+	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	Escherichia coli
NADP+	electron density analysis of binding site. The enzyme activity measured in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	Escherichia coli K-12

Crystallization (Commentary) (protein specific)

Crystallization	Organism
comparison to human enzyme, analysis of NADP+ binding site. Enzyme is a homotetramer with the 4 monomers related by a non-crystallographic 222 symmetry. The conserved catalytic site residues and active site residues correspond to C288 and E254 as well as R164, R282 and S445, respectively	Escherichia coli K-12
in complex with NADP+, hanging drop vapour diffusion method, using 0.2 M ammonium tartrate, 26-31% polyethylene glycol 3350, 10 mM beta-mercaptoethanol and 0.1 M Tris (pH 7.2-7.5)	Escherichia coli

KM Value [mM] (protein specific)

KM Value [mM]	KM Value Maximum [mM]	Substrate	Commentary	Organism	Structure
0.01694	-	Succinate semialdehyde	in 100 mM sodium phosphate buffer, pH 8.0, 30°C	Escherichia coli
0.01694	-	Succinate semialdehyde	pH 8.0, 30°C	Escherichia coli K-12

Natural Substrates/ Products (Substrates) (protein specific)

Natural Substrates	Organism	Commentary (Nat. Sub.)	Natural Products	Commentary (Nat. Pro.)	Organism (Nat. Pro.)	Reversibility
succinate semialdehyde + NAD+ + H2O	Escherichia coli	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	succinate + NADH + H+	-	-	?
succinate semialdehyde + NADP+ + H2O	Escherichia coli	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	succinate + NADPH + H+	-	-	?

Purification (Commentary) (protein specific)

Commentary	Organism
nickel chelating Sepharose column chromatography and S200 16/60 gel filtration	Escherichia coli
recombinant enzyme	Escherichia coli K-12

Substrates and Products (Substrate) (protein specific)

Substrates	Commentary Substrates	Literature (Substrates)	Organism	Products	Commentary (Products)	Literature (Products)	Organism (Products)	Reversibility
succinate semialdehyde + NAD+ + H2O	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	710394	Escherichia coli	succinate + NADH + H+	-	-	-	?
succinate semialdehyde + NADP+ + H2O	the enzyme activity in the presence of NADP+ is approximately 20fold higher than that measured in the presence of NAD+	710394	Escherichia coli	succinate + NADPH + H+	-	-	-	?
succinate semialdehyde + NADP+ + H2O	-	710394	Escherichia coli K-12	succinate + NADPH + 2 H+	-	-	-	?

Subunits (protein specific)

Subunits	Commentary	Organism
tetramer	x-ray crystallography	Escherichia coli
tetramer	crystallographic data	Escherichia coli K-12

General Information

General Information	Commentary	Organism
metabolism	SSADH plays an essential role in the metabolism of the inhibitory neurotransmitter c-aminobutyric acid	Escherichia coli

General Information (protein specific)

General Information	Commentary	Organism
metabolism	SSADH plays an essential role in the metabolism of the inhibitory neurotransmitter c-aminobutyric acid	Escherichia coli

See also following references to EC number 1.2.1.79 (sorted by year of publication):

No.	1st author	Pub Med	title	organims	journal	volume	pages	year	Activating Compound	Application	Cloned(Commentary)	Crystallization (Commentary)	Engineering	General Stability	Inhibitors	KM Value [mM]	Localization	Metals/Ions	Molecular Weight [Da]	Natural Substrates/ Products (Substrates)	Organic Solvent Stability	Organism	Oxidation Stability	Posttranslational Modification	Purification (Commentary)	Reaction	Renatured (Commentary)	Source Tissue	Specific Activity [micromol/min/mg]	Storage Stability	Substrates and Products (Substrate)	Subunits	Temperature Optimum [°C]	Temperature Range [°C]	Temperature Stability [°C]	Turnover Number [1/s]	pH Optimum	pH Range	pH Stability	Cofactor	Ki Value [mM]	pI Value	IC50 Value	Activating Compound (protein specific)	Application (protein specific)	Cloned(Commentary) (protein specific)	Cofactor (protein specific)	Crystallization (Commentary) (protein specific)	Engineering (protein specific)	General Stability (protein specific)	IC50 Value (protein specific)	Inhibitors (protein specific)	Ki Value [mM] (protein specific)	KM Value [mM] (protein specific)	Localization (protein specific)	Metals/Ions (protein specific)	Molecular Weight [Da] (protein specific)	Natural Substrates/ Products (Substrates) (protein specific)	Organic Solvent Stability (protein specific)	Oxidation Stability (protein specific)	Posttranslational Modification (protein specific)	Purification (Commentary) (protein specific)	Renatured (Commentary) (protein specific)	Source Tissue (protein specific)	Specific Activity [micromol/min/mg] (protein specific)	Storage Stability (protein specific)	Substrates and Products (Substrate) (protein specific)	Subunits (protein specific)	Temperature Optimum [°C] (protein specific)	Temperature Range [°C] (protein specific)	Temperature Stability [°C] (protein specific)	Turnover Number [1/s] (protein specific)	pH Optimum (protein specific)	pH Range (protein specific)	pH Stability (protein specific)	pI Value (protein specific)	Expression	General Information	General Information (protein specific)	Expression (protein specific)	KCat/KM [mM/s]	KCat/KM [mM/s] (protein specific)
707392	Ahn		Crystal structure of non-redox ...	Escherichia coli	Biochem. Biophys. Res. Commun.	392	106-111	2010	-	-	1	1	-	-	-	-	1	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1	-	1	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
710394	Langendorf		The X-ray crystal structure of ...	Escherichia coli, Escherichia coli K-12	PLoS One	5	e9280	2010	-	1	2	2	-	-	-	2	-	-	-	2	-	3	-	-	2	-	-	-	-	-	3	2	-	-	-	-	-	-	-	4	-	-	-	-	1	2	4	2	-	-	-	-	-	2	-	-	-	2	-	-	-	2	-	-	-	-	3	2	-	-	-	-	-	-	-	-	-	1	1	-	-	-
690736	Jaeger		Saturation transfer difference ...	Escherichia coli	Biochem. Biophys. Res. Commun.	372	400-406	2008	-	-	1	-	-	-	1	2	-	-	-	-	-	1	-	-	-	-	-	-	1	-	9	-	1	-	-	-	1	1	-	2	-	-	1	-	-	1	2	-	-	-	1	1	-	2	-	-	-	-	-	-	-	-	-	-	1	-	9	-	1	-	-	-	1	1	-	-	-	-	-	-	-	-
288054	Lutke-Eversloh		Biochemical and molecular char ...	Cupriavidus necator	FEMS Microbiol. Lett.	181	63-71	1999	-	-	1	-	-	-	-	1	-	-	-	-	-	1	-	-	-	-	-	-	2	-	2	1	1	-	1	-	1	-	-	2	-	-	-	-	-	1	2	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	2	-	2	1	1	-	1	-	1	-	-	-	1	1	1	1	-	-
708907	Bartsch		Molecular analysis of two gene ...	Escherichia coli	J. Bacteriol.	172	7035-7042	1990	-	-	1	-	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	1	1	-	-	-	-	-	-	-	1	-	-	-	-	-	1	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1	1	-	-	-	-	-	-	-	-	1	-	-	1	-	-
288038	Sanchez		Purification and properties of ...	Klebsiella pneumoniae	Biochim. Biophys. Acta	990	225-231	1989	-	-	-	-	-	-	2	2	-	-	1	-	-	1	-	-	-	-	-	-	1	-	1	-	1	-	-	-	1	-	-	1	-	-	-	-	-	-	1	-	-	-	-	2	-	2	-	-	1	-	-	-	-	-	-	-	1	-	1	-	1	-	-	-	1	-	-	-	-	-	-	-	-	-
707583	Sanchez		Properties and functions of tw ...	Pseudomonas putida	Biochim. Biophys. Acta	953	249-257	1988	2	-	-	-	-	-	2	2	-	-	1	-	-	1	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	1	-	-	-	2	-	-	1	-	-	-	-	2	-	2	-	-	1	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	1	-	-	1	-	-
707580	Cozzani		Separation and characterizatio ...	Escherichia coli K-12	Biochim. Biophys. Acta	613	309-317	1980	1	-	-	-	-	-	-	2	-	-	-	-	-	1	-	-	-	-	-	-	-	2	2	-	1	-	2	-	1	-	1	-	-	-	-	1	-	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	-	-	-	2	2	-	1	-	2	-	1	-	1	-	1	-	-	1	-	-
288042	Tokunaga		Separation and properties of t ...	Euglena gracilis	Biochim. Biophys. Acta	429	55-62	1976	1	-	-	-	-	-	8	2	-	1	-	-	-	1	-	-	-	-	-	-	1	1	3	-	1	-	1	-	1	-	-	1	-	-	-	1	-	-	1	-	-	-	-	8	-	2	-	1	-	-	-	-	-	-	-	-	1	1	3	-	1	-	1	-	1	-	-	-	1	-	-	1	-	-