Literature summary for 1.2.1.88 extracted from

Korasick, D.A.; Koncitikova, R.; Kopecna, M.; Hajkova, E.; Vigouroux, A.; Morera, S.; Becker, D.F.; Sebela, M.; Tanner, J.J.; Kopecny, D.
Structural and biochemical characterization of aldehyde dehydrogenase 12, the last enzyme of proline catabolism in plants (2019), J. Mol. Biol., 431, 576-592 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene ALDH12, composed of 15 exons on chromosome 6, phylogenetic analysis, the maize cultivar Cellux cDNA sequence differs in 15 bases leading to five amino acid substitutions (P86S, V88M, A127T, V468I and V532I) compared to the sequenced B73 cultivar, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli	Zea mays
gene ALDH12, composed of 16 exons on chromosome 5, phylogenetic analysis	Physcomitrium patens

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified ZmALDH12 in complex with NAD+, sitting drop vapour diffusion method, mixing of 2 mg/ml protein in 50 mM Tris, pH 7.8, 50 mM NaCl, 0.5 mM tris(2-caboxyethyl)phosphine (TCEP), 1 mM NAD+, and 5% v/v glycerol with a crystallization solution containing 0.09 M sodium nitrate, sodium phosphate, and ammonium sulfate, and a precipitant mixture containing 25% v/v 2-methyl-2,4-pentanediol, 25% w/v PEG 1000, and 25% w/v polyethylene glycol 3350, and 0.1 M Tris/bicine pH 8.5, in a 1:1 ratio v/v, X-ray diffraction structure determination and analysis at 2.20 A resolution, structure modeling using molecular replacement and a search model derived from a betaine ALDH (PDB ID 4MPY)	Zea mays

Crystallization (Comment)

Organism

purified ZmALDH12 in complex with NAD+, sitting drop vapour diffusion method, mixing of 2 mg/ml protein in 50 mM Tris, pH 7.8, 50 mM NaCl, 0.5 mM tris(2-caboxyethyl)phosphine (TCEP), 1 mM NAD+, and 5% v/v glycerol with a crystallization solution containing 0.09 M sodium nitrate, sodium phosphate, and ammonium sulfate, and a precipitant mixture containing 25% v/v 2-methyl-2,4-pentanediol, 25% w/v PEG 1000, and 25% w/v polyethylene glycol 3350, and 0.1 M Tris/bicine pH 8.5, in a 1:1 ratio v/v, X-ray diffraction structure determination and analysis at 2.20 A resolution, structure modeling using molecular replacement and a search model derived from a betaine ALDH (PDB ID 4MPY)

Zea mays

Protein Variants

Protein Variants	Comment	Organism
C330A	site-directed mutagenesis, inactive mutant	Zea mays
D226A	site-directed mutagenesis, the mutant shows altered kinetics compared to wild-type enzyme	Zea mays
E205A	site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme	Zea mays
F202A	site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme	Zea mays
F505A	site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme	Zea mays
K329A	site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme	Zea mays
P86S/V88M/A127T/V468I/V532I	the maize cultivar Cellux cDNA sequence differs in 15 bases leading to five amino acid substitutions compared to the sequenced B73 cultivar, UniProt ID A0A2H4PMI3	Zea mays
S331A	site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme	Zea mays

General Stability

General Stability	Organism
the maize enzyme is greatly stabilized in presence of NaCl	Zea mays
the moss enzyme is not stabilized in presence of NaCl	Physcomitrium patens

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.032	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant E205A	Zea mays
0.071	-	NADP+	pH 7.5, 30°C, recombinant mutant D226A	Zea mays
0.082	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.084	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.119	-	NAD+	pH 7.5, 30°C, recombinant mutant D226A	Zea mays
0.12	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant E205A	Zea mays
0.17	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant F505A	Zea mays
0.173	-	2-aminoadipic semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.185	-	NAD+	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.198	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.211	-	2-aminoadipic semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.227	-	NAD+	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.227	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant S331A	Zea mays
0.228	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.266	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant D226A	Zea mays
0.379	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant F505A	Zea mays
0.442	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant K329A	Zea mays
0.48	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant F202A	Zea mays
0.624	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant S331A	Zea mays
0.958	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant K329A	Zea mays
0.969	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant F202A	Zea mays
1.86	-	D-glyceraldehyde 3-phosphate	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
2.872	-	NADP+	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
3.066	-	NADP+	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
mitochondrion	-	Physcomitrium patens	5739	-
mitochondrion	-	Zea mays	5739	-

Metals/Ions

Metals/Ions	Comment	Organism	Structure
additional information	the moss enzyme is not stabilized in presence of NaCl	Physcomitrium patens
NaCl	the maize enzyme is greatly stabilized in presence of NaCl	Zea mays

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
glutaric semialdehyde + NAD+ + H2O	Physcomitrium patens	-	glutarate + NADH + H+	-	ir
glutaric semialdehyde + NAD+ + H2O	Zea mays	-	glutarate + NADH + H+	-	ir
L-glutamate 5-semialdehyde + NAD+ + H2O	Physcomitrium patens	-	L-glutamate + NADH + H+	-	ir
L-glutamate 5-semialdehyde + NAD+ + H2O	Zea mays	-	L-glutamate + NADH + H+	-	ir

Organism

Organism	UniProt	Comment	Textmining
Physcomitrium patens	A9S190	-	-
Zea mays	A0A2H4PMI3	cultivar Cellux	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by nickel affinity chromatography, gel filtration, and ultrafiltration	Zea mays

Source Tissue

Source Tissue	Comment	Organism	Textmining
leaf	-	Zea mays	-
additional information	analysis of spatial and temporal expression of ALDH12 in maize seedlings and full-grown plant leaves	Zea mays	-
root	-	Zea mays	-
seedling	-	Zea mays	-
shoot	-	Zea mays	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
2-aminoadipic semialdehyde + NAD+ + H2O	about 6% activity compared to L-glutamate 5-semialdehyde	Physcomitrium patens	2-aminoadipate + NADH + H+	-	?
2-aminoadipic semialdehyde + NAD+ + H2O	about 6% activity compared to L-glutamate 5-semialdehyde	Zea mays	2-aminoadipate + NADH + H+	-	?
3-aminopropanal + NAD+ + H2O	-	Physcomitrium patens	3-aminopropanoate + NADH + H+	-	?
3-aminopropanal + NAD+ + H2O	-	Zea mays	3-aminopropanoate + NADH + H+	-	?
4-aminobutanal + NAD+ + H2O	about 5% activity compared to L-glutamate 5-semialdehyde	Physcomitrium patens	4-aminobutanoate + NADH + H+	-	?
4-aminobutanal + NAD+ + H2O	about 5% activity compared to L-glutamate 5-semialdehyde	Zea mays	4-aminobutanoate + NADH + H+	-	?
D-glyceraldehyde 3-phosphate + NAD+ + H2O	about 7.5% activity compared to L-glutamate 5-semialdehyde	Physcomitrium patens	3-phospho-D-glycerate + NADH + H+	-	?
D-glyceraldehyde 3-phosphate + NAD+ + H2O	about 7.5% activity compared to L-glutamate 5-semialdehyde	Zea mays	3-phospho-D-glycerate + NADH + H+	-	?
glutaric semialdehyde + NAD+ + H2O	-	Physcomitrium patens	glutarate + NADH + H+	-	ir
glutaric semialdehyde + NAD+ + H2O	-	Zea mays	glutarate + NADH + H+	-	ir
L-glutamate 5-semialdehyde + NAD+ + H2O	-	Physcomitrium patens	L-glutamate + NADH + H+	-	ir
L-glutamate 5-semialdehyde + NAD+ + H2O	-	Zea mays	L-glutamate + NADH + H+	-	ir
L-glutamate 5-semialdehyde + NAD+ + H2O	NAD+ is the preferred cofactor	Physcomitrium patens	L-glutamate + NADH + H+	-	ir
L-glutamate 5-semialdehyde + NAD+ + H2O	NAD+ is the preferred cofactor	Zea mays	L-glutamate + NADH + H+	-	ir
L-glutamate 5-semialdehyde + NADP+ + H2O	-	Physcomitrium patens	L-glutamate + NADPH + H+	-	ir
L-glutamate 5-semialdehyde + NADP+ + H2O	-	Zea mays	L-glutamate + NADPH + H+	-	ir
additional information	the enzyme shows a narrow substrate preference for L-glutamate 5-semialdehyde (GSAL) and glutaric semialdehyde (GRSAL)	Physcomitrium patens	?	-	-
additional information	the enzyme shows a narrow substrate preference for L-glutamate 5-semialdehyde (GSAL) and glutaric semialdehyde (GRSAL)	Zea mays	?	-	-
phenylacetaldehyde + NAD+ + H2O	about 5% activity compared to L-glutamate 5-semialdehyde	Physcomitrium patens	phenylacetate + NADH + H+	-	?
phenylacetaldehyde + NAD+ + H2O	about 5% activity compared to L-glutamate 5-semialdehyde	Zea mays	phenylacetate + NADH + H+	-	?
phenylpropionaldehyde + NAD+ + H2O	about 5% activity compared to L-glutamate 5-semialdehyde	Physcomitrium patens	phenylpropionate + NADH + H+	-	?
phenylpropionaldehyde + NAD+ + H2O	about 5% activity compared to L-glutamate 5-semialdehyde	Zea mays	phenylpropionate + NADH + H+	-	?
succinic semialdehyde + NAD+ + H2O	about 2% activity compared to L-glutamate 5-semialdehyde	Physcomitrium patens	succinate + NADH + H+	-	?
succinic semialdehyde + NAD+ + H2O	about 2% activity compared to L-glutamate 5-semialdehyde	Zea mays	succinate + NADH + H+	-	?

Subunits

Subunits	Comment	Organism
dimer or tetramer	GSALDH exists in an equilibrium between a domain-swapped dimer and the dimer-of-dimers tetramer	Physcomitrium patens
dimer or tetramer	GSALDH exists in an equilibrium between a domain-swapped dimer and the dimer-of-dimers tetramer	Zea mays

Synonyms

Synonyms	Comment	Organism
aldehyde dehydrogenase 12	-	Physcomitrium patens
aldehyde dehydrogenase 12	-	Zea mays
ALDH12	-	Physcomitrium patens
ALDH12	-	Zea mays
GSALDH	-	Physcomitrium patens
GSALDH	-	Zea mays
NAD+-dependent glutamate gamma-semialdehyde dehydrogenase	-	Physcomitrium patens
NAD+-dependent glutamate gamma-semialdehyde dehydrogenase	-	Zea mays
PpALDH12	-	Physcomitrium patens
ZmALDH12	-	Zea mays

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
30	-	assay at	Zea mays

Temperature Stability [°C]

Temperature Stability Minimum [°C]	Temperature Stability Maximum [°C]	Comment	Organism
53	-	PpALDH12 has the highest Tm of 53.0°C in 150 mM sodium diphosphate, pH 7.5 (containing 5% glycerol)	Physcomitrium patens
75.7	-	ZmALDH12 displays a Tm of 75.7°C in 150 mM Tris-HCl buffer, pH 7.5 (containing 100 mM NaCl and 5% glycerol)	Zea mays

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
0.005	-	2-aminoadipic semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.03	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant F505A	Zea mays
0.04	-	2-aminoadipic semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.05	-	NADP+	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.15	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant F202A	Zea mays
0.17	-	NAD+	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.21	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant E205A	Zea mays
0.21	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant F202A	Zea mays
0.26	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant K329A	Zea mays
0.3	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.31	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant K329A	Zea mays
0.4	-	D-glyceraldehyde 3-phosphate	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.44	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.52	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant F505A	Zea mays
0.53	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant E205A	Zea mays
0.8	-	NADP+	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.89	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant mutant S331A	Zea mays
1.5	-	NADP+	pH 7.5, 30°C, recombinant mutant D226A	Zea mays
1.7	-	NAD+	pH 7.5, 30°C, recombinant mutant D226A	Zea mays
1.83	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant S331A	Zea mays
1.9	-	Glutaric semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
3.1	-	NAD+	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
3.6	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant D226A	Zea mays
6.8	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	-	Physcomitrium patens
7.5	-	-	Zea mays

Cofactor

Cofactor	Comment	Organism
additional information	the apparent catalytic efficiency for NAD+ is about 60fold higher than for NADP+	Zea mays
NAD+	-	Physcomitrium patens
NAD+	binding structure analysis, modeling	Zea mays

Expression

Organism	Comment	Expression
Zea mays	ALDH12 expression in maize is downregulated in response to salt and drought stresses, possibly to maintain proline levels. Maize seedlings are also exposed to exogenous proline and arginine, and although ZmALDH12 transcript levels in roots do not significantly differ, ZmALDH12 levels in maize leaves are significantly altered: transcript levels are 5fold higher in response to arginine, but nearly 100fold lower in response to proline. This result may indicate an increased contribution of arginine catabolism to cellular glutamate in leaves. Addition of exogenous glutamate results in decreased ZmALDH12 expression in the shoot and increased expression in roots	down
Physcomitrium patens	ALDH12 expression in moss is downregulated in response to salt and drought stresses, possibly to maintain proline levels, with 200 mM NaCl or 400 mM sorbitol, PpALDH12 transcript levels are reduced	down
Zea mays	although ZmALDH12 transcript levels in roots do not significantly differ, ZmALDH12 levels in maize leaves are significantly altered: transcript levels are 5fold higher in response to arginine, but nearly 100fold lower in response to proline. This result may indicate an increased contribution of arginine catabolism to cellular glutamate in leaves. Addition of exogenous glutamate results in decreased ZmALDH12 expression in the shoot and increased expression in roots	up

General Information

General Information	Comment	Organism
evolution	plant GSALDHs of the ALDH12 family share very low sequence identity with bacterial, fungal, and animal GSALDHs (classified as ALDH4), which are the closest related ALDH superfamily members. Nearly all key residues involved in the recognition of GSAL are identical to those in ALDH4, indicating a close functional relationship with ALDH4. Phylogenetic analysis of the ALDH4 and ALDH12 families suggests that the transition from ALDH4 to ALDH12 occurred during the evolution of the endosymbiotic plant ancestor, prior to the evolution of green algae and land plants	Physcomitrium patens
evolution	plant GSALDHs of the ALDH12 family share very low sequence identity with bacterial, fungal, and animal GSALDHs (classified as ALDH4), which are the closest related ALDH superfamily members. Nearly all key residues involved in the recognition of GSAL are identical to those in ALDH4, indicating a close functional relationship with ALDH4. Phylogenetic analysis of the ALDH4 and ALDH12 families suggests that the transition from ALDH4 to ALDH12 occurred during the evolution of the endosymbiotic plant ancestor, prior to the evolution of green algae and land plants	Zea mays
additional information	enzyme structure comparisons	Zea mays
physiological function	ALDH12 encodes an NAD+-dependent glutamate gamma-semialdehyde dehydrogenase (GSALDH), which irreversibly converts glutamate gamma -semialdehyde (GSAL), a mitochondrial intermediate of the proline and arginine catabolism, to glutamate	Physcomitrium patens
physiological function	ALDH12 encodes an NAD+-dependent glutamate gamma-semialdehyde dehydrogenase (GSALDH), which irreversibly converts glutamate gamma -semialdehyde (GSAL), a mitochondrial intermediate of the proline and arginine catabolism, to glutamate	Zea mays

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
0.016	-	NADP+	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.024	-	2-aminoadipic semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
0.155	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant F202A	Zea mays
0.18	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant F505A	Zea mays
0.22	-	D-glyceraldehyde 3-phosphate	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.23	-	2-aminoadipic semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.27	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant K329A	Zea mays
0.28	-	NADP+	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
0.75	-	NAD+	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
1.75	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant E205A	Zea mays
1.93	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Physcomitrium patens
2.93	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant S331A	Zea mays
13.53	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant mutant D226A	Zea mays
14.29	-	NAD+	pH 7.5, 30°C, recombinant mutant D226A	Zea mays
16.76	-	NAD+	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays
21.13	-	NADP+	pH 7.5, 30°C, recombinant mutant D226A	Zea mays
34.34	-	L-glutamate 5-semialdehyde	pH 7.5, 30°C, recombinant wild-type enzyme	Zea mays