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Information on EC 1.4.1.9 - leucine dehydrogenase and Organism(s) Geobacillus stearothermophilus and UniProt Accession P13154

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EC Tree
     1 Oxidoreductases
         1.4 Acting on the CH-NH2 group of donors
             1.4.1 With NAD+ or NADP+ as acceptor
                1.4.1.9 leucine dehydrogenase
IUBMB Comments
Also acts on isoleucine, valine, norvaline and norleucine.
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This record set is specific for:
Geobacillus stearothermophilus
UNIPROT: P13154
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Word Map
The taxonomic range for the selected organisms is: Geobacillus stearothermophilus
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
leucine dehydrogenase, leudh, l-leucine dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dehydrogenase, leucine
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-
-
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L-leucine dehydrogenase
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-
-
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L-leucine:NAD+ oxidoreductase, deaminating
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-
-
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LeuDH
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-leucine + H2O + NAD+ = 4-methyl-2-oxopentanoate + NH3 + NADH + H+
show the reaction diagram
ordered bi-ter mechanism, in which NAD+ and L-Leu are bound and NH4+, 2-oxoisohexanoate, and NADH are released in that order
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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oxidation
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reduction
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SYSTEMATIC NAME
IUBMB Comments
L-leucine:NAD+ oxidoreductase (deaminating)
Also acts on isoleucine, valine, norvaline and norleucine.
CAS REGISTRY NUMBER
COMMENTARY hide
9082-71-7
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
alpha-keto beta-methylvalerate + NH3 + NADH + H+
L-isoleucine + H2O + NAD+
show the reaction diagram
yield: 95%
-
-
?
alpha-ketocaproate + NH3 + NADH + H+
L-norleucine + H2O + NAD+
show the reaction diagram
yield: 80%
-
-
?
alpha-ketoisocaproate + NH3 + NADH + H+
L-leucine + H2O + NAD+
show the reaction diagram
yield: 92.5%
-
-
?
alpha-ketoisovalerate + NH3 + NADH + H+
L-valine + H2O + NAD+
show the reaction diagram
yield: 90%
-
-
?
alpha-ketovalerate + NH3 + NADH + H+
L-norvaline + H2O + NAD+
show the reaction diagram
yield: 92%
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-
?
2-keto-beta-methylvalerate + NH3 + NADH
? + H2O + NAD+
show the reaction diagram
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as active as 2-ketoisocaproate, wild-type enzyme
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-
?
2-keto-gamma-methylthiobutanoate + NH3 + NADH
L-Met + H2O + NAD+
show the reaction diagram
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15% of the activity with 2-ketoisocaproate, wild-type enzyme
-
-
?
2-ketobutyrate + NH3 + NADH
L-2-aminobutyrate + H2O + NAD+
show the reaction diagram
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47% of the activity with 2-ketoisocaproate, wild-type enzyme
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-
?
2-ketoisocaproate + NH3 + NADH
L-Ile + H2O + NAD+
show the reaction diagram
-
-
-
-
?
2-ketovalerate + NH3 + NADH
L-norvaline + H2O + NAD+
show the reaction diagram
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86% of the activity with 2-ketoisocaproate, wild-type enzyme
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-
?
2-oxo-4-methylselenobutyrate + NH3 + NADH
L-selenomethionine + H2O + NAD+
show the reaction diagram
-
-
-
?
2-oxohexanoate + NH3 + NADH + H+
L-norleucine + H2O + NAD+
show the reaction diagram
-
-
-
-
r
L-Ile + H2O + NAD+
3-methyl-2-oxopentanoate + NH3 + NADH
show the reaction diagram
L-Leu + H2O + NAD+
4-methyl-2-oxopentanoate + NH3 + NADH
show the reaction diagram
L-Met + H2O + NAD+
4-methylthio-2-oxobutyrate + NH3 + NADH + H+
show the reaction diagram
L-norleucine + H2O + NAD+
? + NH3 + NADH
show the reaction diagram
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14% the activity with L-Leu, wild-type enzyme
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-
?
L-norvaline + H2O + NAD+
2-ketovalerate + NH3 + NADH
show the reaction diagram
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56% the activity with L-Leu, wild-type enzyme
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-
?
L-Phe + H2O + NAD+
phenylpyruvate + NH3 + NADH
show the reaction diagram
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no activity of wild-type enzyme activity with mutant enzymes A113G, A113G/V291L
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-
?
L-Val + H2O + NAD+
3-methyl-2-oxobutanoate + NH3 + NADH
show the reaction diagram
phenylpyruvate + NH3 + NADH
L-Phe + H2O + NAD+
show the reaction diagram
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15% of the activity with 2-ketoisocaproate, wild-type enzyme
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-
?
additional information
?
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substrate specificity of the chimeric enzyme consisting of an amino-terminal domain of phenylalanine dehydrogenase and a carboxy-terminal domain of leucine dehydrogenase
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4-methyl-2-pentanone
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competitive inhibition of wild-type enzyme, noncompetitive inhibition of mutant enzyme K80A
4-methylpentanoate
Cu(CH3COO)2
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1 mM, 20% inhibition
Cu2+
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1 mM CuCl2, 22% inhibition
HgCl2
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0.01 M, 65% inhibition
Pb(CH3COO)2
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1 mM, 20% inhibition
PCMB
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0.01 M, 50% inhibition
pyridoxal 5'-phosphate
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
13
2-oxo-4-methylselenobutanoate
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-
2 - 28
2-Oxohexanoate
0.88 - 25
2-Oxoisohexanoate
1.2 - 140
4-methyl-2-oxopentanoate
3.8 - 69
alpha-keto-beta-methylvalerate
0.88 - 30
alpha-keto-isocaproate
2.4 - 33
L-Ile
1.4 - 130
L-Leu
4.1 - 24
L-norleucine
7.8 - 70
L-norvaline
31 - 66
L-Phe
0.034 - 17
NAD+
0.017 - 0.055
NADH
75 - 750
NH4+
7.1 - 9.9
phenylpyruvate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
24 - 140
2-Oxohexanoate
37 - 280
alpha-keto-beta-methylvalerate
29 - 280
alpha-keto-isocaproate
1.4 - 23
L-Ile
0.74 - 50
L-Leu
0.6 - 18
L-norleucine
0.29 - 13
L-norvaline
0.8 - 1.4
L-Phe
9.9 - 22
phenylpyruvate
additional information
additional information
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
140
4-methyl-2-pentanone
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wild-type enzyme
20 - 33
4-methylpentanoate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
11
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oxidative deamination of L-Leu
8.8
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reductive amination of 3-methyl-2-oxobutanoate
additional information
-
pH-optima for the chimeric enzyme consisting of an amino-terminal domain of phenylalanine dehydrogenase and a carboxy-terminal domain of leucine dehydrogenase
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.7 - 10.7
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pH 8.7: about 65% of maximal activity, pH 10.7: about 45% of maximal activity, reductive amination of 2-oxo-4-methylselenobutanoate
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
68 - 70
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oxidative amination of L-Leu
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50 - 80
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50°C: 37% of maximal activity, 80°C: 55% of maximal activity, oxidative amination of L-Leu
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
DHLE_GEOSE
367
0
40458
Swiss-Prot
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
300000
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gel filtration
40000
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2 * 40000, SDS-PAGE
46903
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x * 46903, calculation from nucleotide sequence
49000
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6 * 49000, SDS-PAGE
additional information
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MW of the chimeric enzyme consisting of an amino-terminal domain of phenylalanine dehydrogenase and a carboxy-terminal domain of leucine dehydrogenase is 72000 Da, determined by gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
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x * 46903, calculation from nucleotide sequence
dimer
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2 * 40000, SDS-PAGE
hexamer
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6 * 49000, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
cryo-electron microscopy structures of apo and NAD+-bound LDH at 3.0 and 3.2 A resolution, respectively. A partial conformational change is triggered by the interaction between Ser147 and the nicotinamide moiety of NAD+. NAD+ binding also enhances the strength of oligomerization interfaces formed by the core domains
structure of apo-protein and in complex with NAD+, to 3.0 and 3.2 A resolution, respectively. NAD+ binds to domain II (residues 137-331), and the NAD+-bound form has a disordered region (residues 142-144) in the loop between domains I and II
A0A0K2HC96
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A94E
proportion of residual activity of A94E is 19% of that of wild type after incubation at 70 °C for 10 min
Y127N
proportion of residual activity of Y127N is 27% of that of wild type after incubation at 70 °C for 10 min
A113G
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mutant enzyme with altered substrate specificity. 17.9fold decrease in turnover number for L-Leu, 1.2fold decrease in turnover-number for L-Ile, 13.8fold increase in turnover number of L-norleucine, 1.7fold decrease in turnover-number for L-norvaline, 3fold decrease in turnover number for alpha-keto-isocaproate, 1.2fold decrease in turnover number for alpha-ketocaproate, 1.3fold increase in turnover number for alpha-ketocaproate, 3.6fold decrease in Km-value for L-Leu, 3.3fold increase in Km-value for L-Ile, 1.1fold decrease in Km-value for L-norleucine, 3.5fold increase in Km-value for L-norvaline, 1.9fold increase in Km-value for alpha-keto-isocaproate, 2.5fold increase in Km-value for alpha-keto-beta-methylvalerate, 2.4fold decrease in Km-value for alpha-ketocaproate, 1.2fold increase in Km-value for NAD+, 1.2fold increase in Km-value for NADH as compared to wild-type enzyme. L-Ethionine and L-Phe are not substrates of the wild-type enzyme but are deaminated by mutant enzyme. Phenylpyruvate is not a substrate of the wild-type enzyme, but is aminated by mutant enzyme
A113G/V291L
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mutant enzyme with altered substrate specificity. 67.6fold decrease in turnover number for L-Leu, 20fold decrease in turnover-number for L-Ile, 2.2fold decrease in turnover number of L-norleucine, 44.8fold decrease in turnover-number for L-norvaline, 9.7fold decrease in turnover number for alpha-keto-isocaproate, 7.6fold decrease in turnover number for alpha-ketocaproate, 4.6fold decrease in turnover number for alpha-ketocaproate, 6.9fold increase in Km-value for L-Leu, 13.8fold increase in Km-value for L-Ile, 5.5fold increase in Km-value for L-norleucine, 9fold increase in Km-value for L-norvaline, 34fold increase in Km-value for alpha-keto-isocaproate, 18.2fold increase in Km-value for alpha-keto-beta-methylvalerate, 6fold increase in Km-value for alpha-ketocaproate, 4.4fold increase in Km-value for NAD+, 2fold decrease in Km-value for NADH as compared to wild-type enzyme. L-Ethionine and L-Phe are not substrates of the wild-type enzyme but are deaminated by mutant enzyme. Phenylpyruvate is not a substrate of the wild-type enzyme, but is aminated by mutant enzyme
G77A
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turnover numver in oxidative deamination of L-Leu is 36% of that of the wild-type enzyme. In reductive amination the turnover number is comparable to that of the wild-type enzyme. The Km-value for 2-oxoisohexanoate is 6.3fold higher and the Km-value for NH4+ is 2.8fold higher than that of the wild-type enzyme. Mutant enzyme shows lowered unfolding temperature compared with the wild-type enzyme. Faster degradation than wild-type enzyme after incubation at 37°C for 15 h with trypsin or subtilisin at a protease-to-substrate ratio of 1:1
G78A
-
turnover number in oxidative deamination of L-Leu is 5.4% of that of the wild-type enzyme. In reductive amination the turnover number is comparable to that of the wild-type enzyme. The Km-value for 2-oxoisohexanoate is 8.8fold higher and the Km-value for NH4+ is 10fold higher than that of the wild-type enzyme. Mutant enzyme shows lowered unfolding temperature compared with the wild-type enzyme. Faster degradation than wild-type enzyme after incubation at 37°C for 15 h with trypsin or subtilisin at a protease-to-substrate ratio of 1:1
G79A
-
turnover number in oxidative deamination of L-Leu is 40% of that of the wild-type enzyme. In reductive amination the turnover number is comparable to that of the wild-type enzyme. The Km-value for 2-oxoisohexanoate is 6.4fold higher and the Km-value for NH4+ is 3.9fold higher than that of the wild-type enzyme. Mutant enzyme shows lowered unfolding temperature compared with the wild-type enzyme
K68A
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nearly complete loss of activity in the oxidative deamination, marked increase in Km-values for both amino acid substrates and oxo acid substrates. An ionizable group in the wild-type enzyme with a pKa value of 10.1-10.7, which must be protonated for binding of substrate and competitive inhibitor with an alpha-carboxyl group, is unobservable in mutant enzyme
K68R
-
nearly complete loss of activity in the oxidative deamination. An ionizable group in the wild-type enzyme with a pKa value of 10.1-10.7, which must be protonated for binding of substrate and competitive inhibitor with an alpha-carboxyl group, is unobservable in mutant enzyme
K80A
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markedly reduced activity in oxidative deamination, nearly 90% of the wild-type activity in reductive amination. Km-value for 2-oxoisohexanoate is 11fold higher than that of the wild-type enzyme, Km-value for L-Leu is lower than that of the wild-type enzyme
K80Q
-
markedly reduced activity in oxidative deamination. Km-value for 2-oxoisohexanoate is 28fold higher than that of the wild-type enzyme, Km-value for L-Leu is about 3times larger than that of the wild-type enzyme
K80R
-
markedly reduced activity in oxidative deamination, 0.6% of the wild-type activity in reductive amination, Km-value for L-Leu is lower than that of the wild-type enzyme
additional information
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 10
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55°C, 5 min, stable
349662
6 - 11
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55°C, 10 min, stable
349674
7 - 11.2
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25°C, 30 min, wild-type enzyme and mutant enzymes K80A, K80R and K80Q
349691
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
80
the residual activity of NAD+-bound form is approximately three times higher than that of the apo form after incubation at 80°C
50
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60 min, enzyme retains more than 75% of its activity
53
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unfolding temperature of mutant enzyme G78A
54
-
pH 7.0-9.5, 60 min, chimeric enzyme consisting of an amino-terminal domain of phenylalanine dehydrogenase and a carboxy-terminal domain of leucine dehydrogenase, stable
55
-
pH 6.0-11.0, 10 min, stable
58
-
pH 7.0-9.5, 60 min, chimeric enzyme consisting of an amino-terminal domain of phenylalanine dehydrogenase and a carboxy-terminal domain of leucine dehydrogenase, loss of activity
60
-
unfolding temperature of mutant enzyme G77A
75
-
unfolding temperature of mutant enzyme K80A
76
-
unfolding temperature of mutant enzyme G79A
79
-
unfolding temperature of mutant enzyme K80R and K80Q
additional information
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
mutant enzymes G77A and G78A show faster degradation than wild-type enzyme after incubation at 37°C for 15 h with trypsin or subtilisin at a protease-to-substrate ratio of 1:1. Wild-type enzyme and mutant enzyme G79A are degraded at almost the same rate
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, buffer containing 0.02% sodium azide, stable for more than 1 year
-
4°C, stable for at least 1 month
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
chimeric enzyme consisting of an amino-terminal domain of phenylalanine dehydrogenase and a carboxy-terminal domain of leucine dehydrogenase
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mutant enzymes K68A and K68R
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one-step purification of recombinant enzyme
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recombinant enzyme
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
overexpressed in Escherichia coli
chimeric enzyme consisting of an amino-terminal domain of phenylalanine dehydrogenase and a carboxy-terminal domain of leucine dehydrogenase
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expression in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
an efficient stereospecific enzymatic synthesis of L-valine, L-leucine, L-norvaline, L-norleucine and L-isoleucine from the corresponding alpha-keto acids by coupling the reactions catalysed by leucine dehydrogenase and glucose dehydrogenase/galactose mutarotase. Giving high yields of L-amino acids, the procedure is economical and easy to perform and to monitor at a synthetically useful scale (1-10 g)
analysis
-
postcolumn co-immobilized leucine dehydrogenase-NADH oxidase reactor for the determination of branched-chain amino acids by high-performance liquid chromatography with chemiluminescence detection
synthesis
-
synthesis of L-selenomethionine from 2-oxo-4-methylselenobutanoate
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kataoka, K.; Takada, H.; Tanizawa, K.; Yoshimura, T.; Esaki, N.; Ohshima, T.; Soda, K.
Construction and characterization of chimeric enzyme consisting of an amino-terminal domain of phenylalanine dehydrogenase and a carboxy-terminal domain of leucine dehydrogenase
J. Biochem.
116
931-936
1994
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Ohshima, T.; Nagata, S.; Soda, K.
Purification and characterization of thermostable leucine dehydrogenase from Bacillus stearothermophilus
Arch. Microbiol.
141
407-411
1985
Geobacillus stearothermophilus
-
Manually annotated by BRENDA team
Nagata, S.; Tanizawa, K.; Esaki, N.; Sakamoto, Y.; Ohshima, T.; Tanaka, H.; Soda, K.
Gene cloning and sequence determination of leucine dehydrogenase from Bacillus stearothermophilus and structural comparison with other NAD(P)+-dependent dehydrogenases
Biochemistry
27
9056-9062
1988
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Oka, M.; Yang, Y.S.; Nagata, S.; Esaki, N.; Tanaka, H.; Soda, K.
Overproduction of thermostable leucine dehydrogenase of Bacillus stearothermophilus and its one-step purification from recombinant cells of Escherichia coli
Biotechnol. Appl. Biochem.
11
307-311
1989
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Esaki, N.; Shimoi, H.; Yang, Y.S.; Tanaka, H.; Soda, K.
Enantioselective synthesis of L-selenomethionine with leucine dehydrogenase
Biotechnol. Appl. Biochem.
11
312-317
1989
Geobacillus stearothermophilus
-
Manually annotated by BRENDA team
Sekimoto, T.; Fukui, T.; Tanizawa, K.
Role of the conserved glycyl residues located at the active site of leucine dehydrogenase from Bacillus stearothermophilus
J. Biochem.
116
176-182
1994
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Kiba, N.; Oyama, Y.; Kato, A.; Furusawa, M.
Postcolumn co-immobilized leucine dehydrogenase-NADH oxidase reactor for the determination of branched-chain amino acids by high-performance liquid chromatography with chemiluminescence detection
J. Chromatogr. A
724
354-357
1996
Geobacillus stearothermophilus
-
Manually annotated by BRENDA team
Sekimoto, T.; Fukui, T.; Tanizawa, K.
Involvement of conserved lysine 68 of Bacillus stearothermophilus leucine dehydrogenase in substrate binding
J. Biol. Chem.
269
7262-7266
1994
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Sekimoto, T.; Matsuyama, T.; Fukui, T.; Tanizawa, K.
Evidence for lysine 80 as general base catalyst of leucine dehydrogenase
J. Biol. Chem.
268
27039-27045
1993
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Oikawa, T.; Kataoka, K.; Jin, Y.; Suzuki, S.; Soda, K.
Fragmentary form of thermostable leucine dehydrogenase of Bacillus stearothermophilus: its construction and reconstitution of active fragmentary enzyme
Biochem. Biophys. Res. Commun.
280
1177-1182
2001
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Kataoka, K.; Tanizawa, K.
Alteration of substrate specificity of leucine dehydrogenase by site-directed mutagenesis
J. Mol. Catal. B
23
299-309
2003
Geobacillus stearothermophilus
-
Manually annotated by BRENDA team
Chiriac, M.; Lupan, I.; Bucurenci, N.; Popescu, O.; Palibroda, N.
Stereoselective synthesis of L-[15N] amino acids with glucose dehydrogenase and galactose mutarotase as NADH regenerating system
J. Labelled Compd. Radiopharm.
51
171-174
2008
Geobacillus stearothermophilus (P13154)
-
Manually annotated by BRENDA team
Yamaguchi, H.; Kamegawa, A.; Nakata, K.; Kashiwagi, T.; Mizukoshi, T.; Fujiyoshi, Y.; Tani, K.
Structural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopy
J. Struct. Biol.
205
11-21
2019
Geobacillus stearothermophilus (P13154), Geobacillus stearothermophilus
Manually annotated by BRENDA team
Yamaguchi, H.; Kamegawa, A.; Nakata, K.; Kashiwagi, T.; Fujiyoshi, Y.; Tani, K.; Mizukoshi, T.
Leucine Dehydrogenase structure and thermostability
Subcell. Biochem.
96
355-372
2021
Geobacillus stearothermophilus (A0A0K2HC96), Geobacillus stearothermophilus, Geobacillus stearothermophilus DSM 13240 (A0A0K2HC96)
Manually annotated by BRENDA team