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Literature summary 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 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.2.1.88 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
1.2.1.88 gene ALDH12, composed of 16 exons on chromosome 5, phylogenetic analysis Physcomitrium patens

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.2.1.88 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

EC Number Protein Variants Comment Organism
1.2.1.88 C330A site-directed mutagenesis, inactive mutant Zea mays
1.2.1.88 D226A site-directed mutagenesis, the mutant shows altered kinetics compared to wild-type enzyme Zea mays
1.2.1.88 E205A site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme Zea mays
1.2.1.88 F202A site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme Zea mays
1.2.1.88 F505A site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme Zea mays
1.2.1.88 K329A site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme Zea mays
1.2.1.88 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
1.2.1.88 S331A site-directed mutagenesis, the mutant shows reduced activity compared to wild-type enzyme Zea mays

General Stability

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

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.2.1.88 0.032
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant E205A Zea mays
1.2.1.88 0.071
-
 NADP+ pH 7.5, 30°C, recombinant mutant D226A Zea mays
1.2.1.88 0.082
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.084
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.119
-
 NAD+ pH 7.5, 30°C, recombinant mutant D226A Zea mays
1.2.1.88 0.12
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant E205A Zea mays
1.2.1.88 0.17
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant F505A Zea mays
1.2.1.88 0.173
-
 2-aminoadipic semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.185
-
 NAD+ pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.198
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.211
-
 2-aminoadipic semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.227
-
 NAD+ pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.227
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant S331A Zea mays
1.2.1.88 0.228
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.266
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant D226A Zea mays
1.2.1.88 0.379
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant F505A Zea mays
1.2.1.88 0.442
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant K329A Zea mays
1.2.1.88 0.48
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant F202A Zea mays
1.2.1.88 0.624
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant S331A Zea mays
1.2.1.88 0.958
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant K329A Zea mays
1.2.1.88 0.969
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant F202A Zea mays
1.2.1.88 1.86
-
 D-glyceraldehyde 3-phosphate pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 2.872
-
 NADP+ pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 3.066
-
 NADP+ pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens

Localization

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

Metals/Ions

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

Natural Substrates/ Products (Substrates)

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

Organism

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

Purification (Commentary)

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

Source Tissue

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

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.2.1.88 2-aminoadipic semialdehyde + NAD+ + H2O about 6% activity compared to L-glutamate 5-semialdehyde Physcomitrium patens 2-aminoadipate + NADH + H+
-
 ?
1.2.1.88 2-aminoadipic semialdehyde + NAD+ + H2O about 6% activity compared to L-glutamate 5-semialdehyde Zea mays 2-aminoadipate + NADH + H+
-
 ?
1.2.1.88 3-aminopropanal + NAD+ + H2O
-
 Physcomitrium patens 3-aminopropanoate + NADH + H+
-
 ?
1.2.1.88 3-aminopropanal + NAD+ + H2O
-
 Zea mays 3-aminopropanoate + NADH + H+
-
 ?
1.2.1.88 4-aminobutanal + NAD+ + H2O about 5% activity compared to L-glutamate 5-semialdehyde Physcomitrium patens 4-aminobutanoate + NADH + H+
-
 ?
1.2.1.88 4-aminobutanal + NAD+ + H2O about 5% activity compared to L-glutamate 5-semialdehyde Zea mays 4-aminobutanoate + NADH + H+
-
 ?
1.2.1.88 D-glyceraldehyde 3-phosphate + NAD+ + H2O about 7.5% activity compared to L-glutamate 5-semialdehyde Physcomitrium patens 3-phospho-D-glycerate + NADH + H+
-
 ?
1.2.1.88 D-glyceraldehyde 3-phosphate + NAD+ + H2O about 7.5% activity compared to L-glutamate 5-semialdehyde Zea mays 3-phospho-D-glycerate + NADH + H+
-
 ?
1.2.1.88 glutaric semialdehyde + NAD+ + H2O
-
 Physcomitrium patens glutarate + NADH + H+
-
 ir
1.2.1.88 glutaric semialdehyde + NAD+ + H2O
-
 Zea mays glutarate + NADH + H+
-
 ir
1.2.1.88 L-glutamate 5-semialdehyde + NAD+ + H2O
-
 Physcomitrium patens L-glutamate + NADH + H+
-
 ir
1.2.1.88 L-glutamate 5-semialdehyde + NAD+ + H2O
-
 Zea mays L-glutamate + NADH + H+
-
 ir
1.2.1.88 L-glutamate 5-semialdehyde + NAD+ + H2O NAD+ is the preferred cofactor Physcomitrium patens L-glutamate + NADH + H+
-
 ir
1.2.1.88 L-glutamate 5-semialdehyde + NAD+ + H2O NAD+ is the preferred cofactor Zea mays L-glutamate + NADH + H+
-
 ir
1.2.1.88 L-glutamate 5-semialdehyde + NADP+ + H2O
-
 Physcomitrium patens L-glutamate + NADPH + H+
-
 ir
1.2.1.88 L-glutamate 5-semialdehyde + NADP+ + H2O
-
 Zea mays L-glutamate + NADPH + H+
-
 ir
1.2.1.88 additional information the enzyme shows a narrow substrate preference for L-glutamate 5-semialdehyde (GSAL) and glutaric semialdehyde (GRSAL) Physcomitrium patens ?
-
-
1.2.1.88 additional information the enzyme shows a narrow substrate preference for L-glutamate 5-semialdehyde (GSAL) and glutaric semialdehyde (GRSAL) Zea mays ?
-
-
1.2.1.88 phenylacetaldehyde + NAD+ + H2O about 5% activity compared to L-glutamate 5-semialdehyde Physcomitrium patens phenylacetate + NADH + H+
-
 ?
1.2.1.88 phenylacetaldehyde + NAD+ + H2O about 5% activity compared to L-glutamate 5-semialdehyde Zea mays phenylacetate + NADH + H+
-
 ?
1.2.1.88 phenylpropionaldehyde + NAD+ + H2O about 5% activity compared to L-glutamate 5-semialdehyde Physcomitrium patens phenylpropionate + NADH + H+
-
 ?
1.2.1.88 phenylpropionaldehyde + NAD+ + H2O about 5% activity compared to L-glutamate 5-semialdehyde Zea mays phenylpropionate + NADH + H+
-
 ?
1.2.1.88 succinic semialdehyde + NAD+ + H2O about 2% activity compared to L-glutamate 5-semialdehyde Physcomitrium patens succinate + NADH + H+
-
 ?
1.2.1.88 succinic semialdehyde + NAD+ + H2O about 2% activity compared to L-glutamate 5-semialdehyde Zea mays succinate + NADH + H+
-
 ?

Subunits

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

Synonyms

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

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.2.1.88 30
-
 assay at Zea mays

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
1.2.1.88 53
-
 PpALDH12 has the highest Tm of 53.0°C in 150 mM sodium diphosphate, pH 7.5 (containing 5% glycerol) Physcomitrium patens
1.2.1.88 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]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.2.1.88 0.005
-
 2-aminoadipic semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.03
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant F505A Zea mays
1.2.1.88 0.04
-
 2-aminoadipic semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.05
-
 NADP+ pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.15
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant F202A Zea mays
1.2.1.88 0.17
-
 NAD+ pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.21
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant E205A Zea mays
1.2.1.88 0.21
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant F202A Zea mays
1.2.1.88 0.26
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant K329A Zea mays
1.2.1.88 0.3
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.31
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant K329A Zea mays
1.2.1.88 0.4
-
 D-glyceraldehyde 3-phosphate pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.44
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.52
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant F505A Zea mays
1.2.1.88 0.53
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant E205A Zea mays
1.2.1.88 0.8
-
 NADP+ pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.89
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant mutant S331A Zea mays
1.2.1.88 1.5
-
 NADP+ pH 7.5, 30°C, recombinant mutant D226A Zea mays
1.2.1.88 1.7
-
 NAD+ pH 7.5, 30°C, recombinant mutant D226A Zea mays
1.2.1.88 1.83
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant S331A Zea mays
1.2.1.88 1.9
-
 Glutaric semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 3.1
-
 NAD+ pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 3.6
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant D226A Zea mays
1.2.1.88 6.8
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Zea mays

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.2.1.88 7.5
-
-
 Physcomitrium patens
1.2.1.88 7.5
-
-
 Zea mays

Cofactor

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

Expression

EC Number Organism Comment Expression
1.2.1.88 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
1.2.1.88 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
1.2.1.88 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

EC Number General Information Comment Organism
1.2.1.88 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
1.2.1.88 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
1.2.1.88 additional information enzyme structure comparisons Zea mays
1.2.1.88 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
1.2.1.88 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]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.2.1.88 0.016
-
 NADP+ pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.024
-
 2-aminoadipic semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 0.155
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant F202A Zea mays
1.2.1.88 0.18
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant F505A Zea mays
1.2.1.88 0.22
-
 D-glyceraldehyde 3-phosphate pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.23
-
 2-aminoadipic semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.27
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant K329A Zea mays
1.2.1.88 0.28
-
 NADP+ pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 0.75
-
 NAD+ pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 1.75
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant E205A Zea mays
1.2.1.88 1.93
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Physcomitrium patens
1.2.1.88 2.93
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant S331A Zea mays
1.2.1.88 13.53
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant mutant D226A Zea mays
1.2.1.88 14.29
-
 NAD+ pH 7.5, 30°C, recombinant mutant D226A Zea mays
1.2.1.88 16.76
-
 NAD+ pH 7.5, 30°C, recombinant wild-type enzyme Zea mays
1.2.1.88 21.13
-
 NADP+ pH 7.5, 30°C, recombinant mutant D226A Zea mays
1.2.1.88 34.34
-
 L-glutamate 5-semialdehyde pH 7.5, 30°C, recombinant wild-type enzyme Zea mays