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Literature summary for 1.4.1.16 extracted from

  • Zhang, Y.; Ma, Q.; Dong, M.; Zhang, X.; Chen, Y.; Gao, X.; Song, Y.
    Essential role of amino acid position 71 in substrate preference by meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum IAM14863 (2018), Enzyme Microb. Technol., 111, 57-62 .
    View publication on PubMed
Search for more literature for 1.4.1.16

Crystallization (Commentary)

Crystallization (Comment) Organism
molecular docking of substrates meso-DAP and pyruvic acid to wild-type and mutant R71A. Substrate binding with meso-DAP or pyruvic acid changes the rigidity of the enzyme and the secondary structure around R71 Symbiobacterium thermophilum

Protein Variants

Protein Variants Comment Organism
A69R mutation to the correspondung residue of Symbiobacteium thermophilum DAPDH. Mutation improves the catalytic efficiencies toward 2-keto acids and does not affect the catalytic efficiency toward meso-DAP Corynebacterium glutamicum
R71A mutation destroys the cation-pi interaction between residues R71 and Y205 Symbiobacterium thermophilum
R71E for reductive amination, the mutant shows a 1.5fold increase in Km and 0.24fold decrease in kcat. For oxidative deamination, a 50% decrease in the kcat/Km value is observed Symbiobacterium thermophilum
R71I R71I shows 0.37fold decrease in kcat/Km value for pyruvic acid Symbiobacterium thermophilum
R71K the kcat/Km values toward pyruvic acid and meso-DAP increase by 1.4fold and 1.8fold, respectively Symbiobacterium thermophilum
R71Q the kcat/Km values toward pyruvic acid and meso-DAP both decrease by 30% Symbiobacterium thermophilum
R71S for pyruvic acid, R71S shows few changes in kcat/Km values Symbiobacterium thermophilum

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.41
-
 meso-2,6-diaminoheptanedioate wild-type, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.43
-
 meso-2,6-diaminoheptanedioate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.43
-
 meso-2,6-diaminoheptanedioate mutant R71S, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.53
-
 meso-2,6-diaminoheptanedioate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.56
-
 meso-2,6-diaminoheptanedioate mutant R71I, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.59
-
 meso-2,6-diaminoheptanedioate mutant R71K, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.63
-
 meso-2,6-diaminoheptanedioate mutant R71Q, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
1.37
-
 meso-2,6-diaminoheptanedioate mutant R71E, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
10.91
-
 pyruvate mutant R71K, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
14.08
-
 pyruvate mutant R71S, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
16.31
-
 pyruvate wild-type, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
19.17
-
 pyruvate mutant R71Q, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
19.24
-
 pyruvate mutant R71I, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
25.18
-
 pyruvate mutant R71E, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
26.88
-
 4-methyl-2-oxopentanoate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
29.92
-
 oxaloacetate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
31.5
-
 oxaloacetate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
33.51
-
 4-methyl-2-oxopentanoate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
36.16
-
 2-oxovalerate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
57.04
-
 2-oxovalerate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
97.88
-
 3-methyl-2-oxobutanoate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
119.2
-
 3-methyl-2-oxobutanoate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
294.9
-
 pyruvate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
337.6
-
 pyruvate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum

Organism

Organism UniProt Comment Textmining
Corynebacterium glutamicum P04964
-
-
Corynebacterium glutamicum ATCC 13032 P04964
-
-
Symbiobacterium thermophilum Q67PI3
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2-oxovalerate + NH3 + NADPH + H+
-
 Corynebacterium glutamicum ? + H2O + NADP+
-
 ?
2-oxovalerate + NH3 + NADPH + H+
-
 Corynebacterium glutamicum ATCC 13032 ? + H2O + NADP+
-
 ?
3-methyl-2-oxobutanoate + NH3 + NADPH + H+
-
 Corynebacterium glutamicum ? + H2O + NADP+
-
 ?
3-methyl-2-oxobutanoate + NH3 + NADPH + H+
-
 Corynebacterium glutamicum ATCC 13032 ? + H2O + NADP+
-
 ?
4-methyl-2-oxopentanoate + NH3 + NADPH + H+
-
 Corynebacterium glutamicum ? + H2O + NADP+
-
 ?
4-methyl-2-oxopentanoate + NH3 + NADPH + H+
-
 Corynebacterium glutamicum ATCC 13032 ? + H2O + NADP+
-
 ?
meso-2,6-diaminoheptanedioate + H2O + NADP+
-
 Corynebacterium glutamicum L-2-amino-6-oxoheptanedioate + NH3 + NADPH + H+
-
 ?
meso-2,6-diaminoheptanedioate + H2O + NADP+
-
 Symbiobacterium thermophilum L-2-amino-6-oxoheptanedioate + NH3 + NADPH + H+
-
 ?
meso-2,6-diaminoheptanedioate + H2O + NADP+
-
 Corynebacterium glutamicum ATCC 13032 L-2-amino-6-oxoheptanedioate + NH3 + NADPH + H+
-
 ?
oxaloacetate + NH3 + NADPH + H+
-
 Corynebacterium glutamicum ? + H2O + NADP+
-
 ?
oxaloacetate + NH3 + NADPH + H+
-
 Corynebacterium glutamicum ATCC 13032 ? + H2O + NADP+
-
 ?
pyruvate + NH3 + NADPH + H+
-
 Corynebacterium glutamicum D-alanine + H2O + NADP+
-
 ?
pyruvate + NH3 + NADPH + H+
-
 Symbiobacterium thermophilum D-alanine + H2O + NADP+
-
 ?

Synonyms

Synonyms Comment Organism
DAPDH
-
 Corynebacterium glutamicum
DAPDH
-
 Symbiobacterium thermophilum
DDH
-
 Corynebacterium glutamicum
Sth1425
-
 Symbiobacterium thermophilum

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.087
-
 oxaloacetate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.1
-
 4-methyl-2-oxopentanoate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.11
-
 oxaloacetate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.12
-
 4-methyl-2-oxopentanoate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.27
-
 3-methyl-2-oxobutanoate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.38
-
 3-methyl-2-oxobutanoate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.91
-
 2-oxovalerate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.93
-
 2-oxovalerate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
1.35
-
 pyruvate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
1.68
-
 pyruvate mutant R71E, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
2.27
-
 pyruvate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
3.09
-
 pyruvate mutant R71I, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
6.15
-
 pyruvate mutant R71Q, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
6.45
-
 pyruvate mutant R71K, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
7
-
 pyruvate wild-type, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
7.2
-
 pyruvate mutant R71S, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
37.44
-
 meso-2,6-diaminoheptanedioate mutant R71S, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
40.47
-
 meso-2,6-diaminoheptanedioate wild-type, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
45.77
-
 meso-2,6-diaminoheptanedioate mutant R71Q, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
50.96
-
 meso-2,6-diaminoheptanedioate mutant R71I, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
51.99
-
 meso-2,6-diaminoheptanedioate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
61.58
-
 meso-2,6-diaminoheptanedioate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
65.62
-
 meso-2,6-diaminoheptanedioate mutant R71E, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
163.6
-
 meso-2,6-diaminoheptanedioate mutant R71K, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.0028
-
 3-methyl-2-oxobutanoate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.0029
-
 oxaloacetate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.0034
-
 4-methyl-2-oxopentanoate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.0046
-
 pyruvate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.016
-
 2-oxovalerate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
0.07
-
 pyruvate mutant R71E, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.16
-
 pyruvate mutant R71I, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.32
-
 pyruvate mutant R71Q, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.43
-
 pyruvate wild-type, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.51
-
 pyruvate mutant R71S, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.59
-
 pyruvate mutant R71K, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
0.96
-
 meso-2,6-diaminoheptanedioate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
1.14
-
 3-methyl-2-oxobutanoate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
1.15
-
 4-methyl-2-oxopentanoate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
1.24
-
 oxaloacetate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
1.46
-
 pyruvate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
1.57
-
 2-oxovalerate mutant A69R, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
47.83
-
 meso-2,6-diaminoheptanedioate mutant R71E, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
72.68
-
 meso-2,6-diaminoheptanedioate mutant R71Q, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
86.73
-
 meso-2,6-diaminoheptanedioate mutant R71S, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
90.84
-
 meso-2,6-diaminoheptanedioate mutant R71I, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
98.48
-
 meso-2,6-diaminoheptanedioate wild-type, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum
120.3
-
 meso-2,6-diaminoheptanedioate wild-type, pH not specified in the publication, temperature not specified in the publication Corynebacterium glutamicum
279.4
-
 meso-2,6-diaminoheptanedioate mutant R71K, pH not specified in the publication, temperature not specified in the publication Symbiobacterium thermophilum