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Information on EC 5.1.1.21 - isoleucine 2-epimerase
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5.1.1.21 isoleucine 2-epimeraseIUBMB Comments
A pyridoxal phosphate protein. The enzyme, characterized from the bacterium Lactobacillus buchneri, specifically catalyses racemization of nonpolar amino acids at the C-2 position.
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Word Map
- 5.1.1.21
- buchneri
-
racemization
- lactobacillus
-
epimerization
- 5'-phosphate
- pyridoxal
-
nonpolar
- d-leucine
- diaminopimelate
-
two-base
- l-isoleucine
- d-valine
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
isoleucine 2-epimerase, plp-independent racemase, branched-chain amino-acid racemase, d-amino acid racemase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
BCAA racemase
isoleucine 2-epimerase
PLP-dependent fold-type I isoleucine 2-epimerase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-isoleucine = D-allo-isoleucine
-
-
-
-
L-isoleucine = D-allo-isoleucine
L-isoleucine epimerization proceeds through abstraction of the alpha-hydrogen of the substrate by Lys280, while Asp222 serves as the catalytic residue adding an alpha-hydrogen to the quinonoid intermediate to form D-allo-isoleucine, structure-function relationship
L-isoleucine = D-allo-isoleucine
the racemization reaction by the fold-type I racemases may generally occur thanks to a revised two-base mechanism. Conformational changes provoked by pyridoxal 5'-phosphate binding suggesting an induced fit of the active site entrance door necessary to accommodate pyridoxal 5'-phosphate and substrate molecules
L-isoleucine = D-allo-isoleucine
the racemization reaction by the fold-type I racemases may generally occur thanks to a revised two-base mechanism. Conformational changes provoked by pyridoxal 5'-phosphate binding suggesting an induced fit of the active site entrance door necessary to accommodate pyridoxal 5'-phosphate and substrate molecules
-
-
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SYSTEMATIC NAME
IUBMB Comments
isoleucine 2-epimerase
A pyridoxal phosphate protein. The enzyme, characterized from the bacterium Lactobacillus buchneri, specifically catalyses racemization of nonpolar amino acids at the C-2 position.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(R)-2-aminobutyric acid
(S)-2-aminobutyric acid
activity is 42% compared to D-allo-isoleucine
-
-
r
(S)-2-aminobutyric acid
(R)-2-aminobutyric acid
activity is 32% compared to L-isoleucine
-
-
r
D-leucine
L-leucine
activity is 30% compared to D-allo-isoleucine
-
-
?
D-methionine
L-methionine
activity is 20% compared to D-allo-isoleucine
-
-
?
D-norleucine
L-norleucine
activity is 59% compared to D-allo-isoleucine
-
-
r
D-phenylalanine
L-phenylalanine
activity is 25% compared to D-allo-isoleucine
-
-
?
D-valine
L-Val
activity is 52% compared to D-allo-isoleucine
-
-
r
L-phenylalanine
D-phenylalanine
activity is 24% compared to L-isoleucine
-
-
?
L-valine
D-Val
activity is 48% compared to L-isoleucine
-
-
r
D-norvaline
L-norvaline
activity is 83% compared to D-allo-isoleucine
-
-
r
D-norvaline
L-norvaline
activity is 83% compared to D-allo-isoleucine
-
-
r
L-leucine
D-leucine
activity is 30% compared to L-isoleucine
-
-
?
L-Methionine
D-Methionine
activity is 19% compared to L-isoleucine
-
-
?
L-Methionine
D-Methionine
activity is 19% compared to L-isoleucine
-
-
?
L-Norleucine
D-Norleucine
activity is 50% compared to L-isoleucine
-
-
r
L-Norleucine
D-Norleucine
activity is 50% compared to L-isoleucine
-
-
r
L-Norvaline
D-Norvaline
activity is 56% compared to L-isoleucine
-
-
r
L-Norvaline
D-Norvaline
activity is 56% compared to L-isoleucine
-
-
r
additional information
?
-
the enzyme does not require pyridoxal 5'-phosphate for its activity. Compared with Ile, DAAR1 shows 1 and 5% relative activity toward Leu and Val, respectively. DAAR1 shows no activity toward N-acetyl-L-Ile, a commercially available surrogate for N-malonyl-L-Ile, suggesting that DAAR1 does not use a N-derivatized substrate
-
-
?
additional information
?
-
-
the enzyme does not require pyridoxal 5'-phosphate for its activity. Compared with Ile, DAAR1 shows 1 and 5% relative activity toward Leu and Val, respectively. DAAR1 shows no activity toward N-acetyl-L-Ile, a commercially available surrogate for N-malonyl-L-Ile, suggesting that DAAR1 does not use a N-derivatized substrate
-
-
?
additional information
?
-
the enzyme specifically catalyzes racemization of nonpolar amino acids at the C-2 position. No activity toward the L- and D-forms of Asp, Glu, Lys, Arg, His, Orn, Thr, Asn, Gln, Trp, and tert-Leu
-
-
?
additional information
?
-
-
the enzyme specifically catalyzes racemization of nonpolar amino acids at the C-2 position. No activity toward the L- and D-forms of Asp, Glu, Lys, Arg, His, Orn, Thr, Asn, Gln, Trp, and tert-Leu
-
-
?
additional information
?
-
the enzyme catalyzes the pyridoxal 5'-phosphate (PLP)-dependent racemization and epimerization of a broad spectrum of nonpolar amino acids from L- to D-form and vice versa, in particular isoleucine
-
-
?
additional information
?
-
-
the enzyme catalyzes the pyridoxal 5'-phosphate (PLP)-dependent racemization and epimerization of a broad spectrum of nonpolar amino acids from L- to D-form and vice versa, in particular isoleucine
-
-
?
additional information
?
-
the enzyme specifically catalyzes racemization of nonpolar amino acids at the C-2 position. No activity toward the L- and D-forms of Asp, Glu, Lys, Arg, His, Orn, Thr, Asn, Gln, Trp, and tert-Leu
-
-
?
additional information
?
-
the enzyme catalyzes the pyridoxal 5'-phosphate (PLP)-dependent racemization and epimerization of a broad spectrum of nonpolar amino acids from L- to D-form and vice versa, in particular isoleucine
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
PLP, a marked structural change occurs around the active site upon binding of pyridoxal 5'-phosphate that provides a solvent-inaccessible environment for the enzymatic reaction
additional information
enzyme does not require pyridoxal 5'-phosphate for its activity
-
additional information
-
enzyme does not require pyridoxal 5'-phosphate for its activity
-
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
hydroxylamine
almost fully inactivated by the first dialysis against buffer containing 50 mM hydroxylamine, after which about 75% of the activity is recovered by a subsequent dialysis against buffer containing 1 mM pyridoxal 5'-phosphate
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
13.2
D-allo-isoleucine
recombinant wild-type enzyme, pH and temperature not specified in the publication
13.8
D-allo-isoleucine
recombinant mutant D222N, pH and temperature not specified in the publication
16
D-allo-isoleucine
recombinant mutant D222A, pH and temperature not specified in the publication
35
D-allo-isoleucine
recombinant mutant Y142F, pH and temperature not specified in the publication
4.46
L-isoleucine
recombinant mutant D222N, pH and temperature not specified in the publication
4.58
L-isoleucine
recombinant mutant D222A, pH and temperature not specified in the publication
5
L-isoleucine
recombinant wild-type enzyme, pH and temperature not specified in the publication
16
L-isoleucine
recombinant mutant Y142F, pH and temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0461
D-allo-isoleucine
recombinant mutant D222N, pH and temperature not specified in the publication
3.56
D-allo-isoleucine
recombinant mutant D222A, pH and temperature not specified in the publication
434
D-allo-isoleucine
recombinant mutant Y142F, pH and temperature not specified in the publication
939
D-allo-isoleucine
recombinant wild-type enzyme, pH and temperature not specified in the publication
0.0238
L-isoleucine
recombinant mutant D222N, pH and temperature not specified in the publication
1.65
L-isoleucine
recombinant mutant D222A, pH and temperature not specified in the publication
279
L-isoleucine
recombinant mutant Y142F, pH and temperature not specified in the publication
502
L-isoleucine
recombinant wild-type enzyme, pH and temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00334
D-allo-isoleucine
recombinant mutant D222N, pH and temperature not specified in the publication
0.223
D-allo-isoleucine
recombinant mutant D222A, pH and temperature not specified in the publication
12.4
D-allo-isoleucine
recombinant mutant Y142F, pH and temperature not specified in the publication
71.4
D-allo-isoleucine
recombinant wild-type enzyme, pH and temperature not specified in the publication
0.00534
L-isoleucine
recombinant mutant D222N, pH and temperature not specified in the publication
0.361
L-isoleucine
recombinant mutant D222A, pH and temperature not specified in the publication
17.5
L-isoleucine
recombinant mutant Y142F, pH and temperature not specified in the publication
101
L-isoleucine
recombinant wild-type enzyme, pH and temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
116
pH 5.5, 37°C, recombinant enzyme, substrate: D-norleucine
149
pH 5.5, 37°C, recombinant enzyme, substrate: L-isoleucine
183
pH 5.5, 37°C, recombinant enzyme, substrate: D-norvaline
221
pH 5.5, 37°C, recombinant enzyme, substrate: D-allo-isoleucine
32
pH 5.5, 37°C, recombinant enzyme, substrate: L-methionine
35.7
pH 5.5, 37°C, recombinant enzyme, substrate: L-phenylalanine
44.2
pH 5.5, 37°C, recombinant enzyme, substrate: L-leucine
44.5
pH 5.5, 37°C, recombinant enzyme, substrate: D-isoleucine
47.7
pH 5.5, 37°C, recombinant enzyme, substrate: (S)-2-aminobutyric acid
54.8
pH 5.5, 37°C, recombinant enzyme, substrate: D-leucine
66.3
pH 5.5, 37°C, recombinant enzyme, substrate: (R)-2-aminobutyric acid
71.7
pH 5.5, 37°C, recombinant enzyme, substrate: L-valine
74.1
pH 5.5, 37°C, recombinant enzyme, substrate: L-norleucine
83.4
pH 5.5, 37°C, recombinant enzyme, substrate: L-norvaline
93.7
pH 5.5, 37°C, recombinant enzyme, substrate: D-methionine
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
45
highest activity for the reaction with D-allo-L-isoleucine
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
a daar1 enzyme knockout mutant shows highly reduced levels of N-malonyl-D-allo-isoleucine
physiological function
the amino acid racemase is responsible for the biosynthesis of N-malonyl-D-allo-isoleucine. DAAR1 does not use a N-derivatized substrate and the malonylation of D-amino acids occurs downstream in the metabolic pathway
additional information
evolution
the enzyme belongs to the fold-type I subgroup of pyridoxal 5'-phosphate-dependent enzymes and is very close to aminobutyrate aminotransferases family
evolution
the enzyme is a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family and belongs to a D-amino acid racemase gene family. The phenazine biosynthesis-like protein family (PF02567), which is closely related to the DAP epimerase (PF01678), proline racemase (PF05544), and PrpF (PF04303) families
evolution
-
the enzyme belongs to the fold-type I subgroup of pyridoxal 5'-phosphate-dependent enzymes and is very close to aminobutyrate aminotransferases family
-
additional information
exploitation of natural metabolic variation by integrating metabolomics with genome-wide association as an approach for functional genomics study of specialized metabolism
additional information
-
exploitation of natural metabolic variation by integrating metabolomics with genome-wide association as an approach for functional genomics study of specialized metabolism
additional information
identification of the active site residues responsible for its nonpolar amino acid recognition and reactivity specificity from structure comparisons with the alpha-amino-epsilon-caprolactam racemase (EC 5.1.1.15) from Achromobacter obae and the cystathionine beta-lyase (EC 4.4.1.8) from Escherichia coli (PDB IDs 2ZUK and 3DXW), active site structure, overview
additional information
-
identification of the active site residues responsible for its nonpolar amino acid recognition and reactivity specificity from structure comparisons with the alpha-amino-epsilon-caprolactam racemase (EC 5.1.1.15) from Achromobacter obae and the cystathionine beta-lyase (EC 4.4.1.8) from Escherichia coli (PDB IDs 2ZUK and 3DXW), active site structure, overview
additional information
the enzyme is a fold-type I racemase, similar to the alpha-amino-epsilon-caprolactam racemase (EC 5.1.1.15). The active-site cavity in the apoenzyme structure is much more solvent-accessible than that in the pyridoxal 5'-phosphate-bound structure. A marked structural change occurs around the active site upon binding of pyridoxal 5'-phosphate that provides a solvent-inaccessible environment for the enzymatic reaction. Detailed enzyme structure analysis and structure comparisons, active site and substrate/ligand-binding structre, structure-function relationship, overview
additional information
-
the enzyme is a fold-type I racemase, similar to the alpha-amino-epsilon-caprolactam racemase (EC 5.1.1.15). The active-site cavity in the apoenzyme structure is much more solvent-accessible than that in the pyridoxal 5'-phosphate-bound structure. A marked structural change occurs around the active site upon binding of pyridoxal 5'-phosphate that provides a solvent-inaccessible environment for the enzymatic reaction. Detailed enzyme structure analysis and structure comparisons, active site and substrate/ligand-binding structre, structure-function relationship, overview
additional information
-
identification of the active site residues responsible for its nonpolar amino acid recognition and reactivity specificity from structure comparisons with the alpha-amino-epsilon-caprolactam racemase (EC 5.1.1.15) from Achromobacter obae and the cystathionine beta-lyase (EC 4.4.1.8) from Escherichia coli (PDB IDs 2ZUK and 3DXW), active site structure, overview
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). K5BJ65_MYCHD
Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)
966
0
102956
TrEMBL
-
A0A644XZN9_9ZZZZ
437
0
48067
TrEMBL
other Location (Reliability: 1)
A0A2R8CEZ4_9RHOB
437
0
47315
TrEMBL
-
A0A644YGX8_9ZZZZ
446
0
48842
TrEMBL
other Location (Reliability: 2)
A0A645BFF7_9ZZZZ
448
0
48832
TrEMBL
other Location (Reliability: 4)
A0A645B378_9ZZZZ
440
0
48937
TrEMBL
other Location (Reliability: 1)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
200000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
tetramer
additional information
tetramer
the enzyme assembles as a tetramer, with each subunit being composed of N-terminal, C-terminal, and large PLP-binding domains
additional information
detailed enzyme structure analysis and structure comparisons, analysis of the structures bound with reaction-intermediate analogues (PLP-L-Ile and PLP-D-allo-Ile), overview
additional information
-
detailed enzyme structure analysis and structure comparisons, analysis of the structures bound with reaction-intermediate analogues (PLP-L-Ile and PLP-D-allo-Ile), overview
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant detagged enzyme in apoform, in complex with pyridoxal 5'-phosphate, in complex with N-(5'-phosphopyridoxyl)-L-isoleucine, and in complex with N-(5'-phosphopyridoxyl)-D-allo-isoleucine. By sitting drop vapour diffusion method, for crystals of PLP-bound enzyme, mixing of 0.002 ml enzyme solution containing 0.05 mM PLP 33% 2-propanol, 0.2 M magnesium acetate, 0.1 M cacodylate buffer pH 6.5, for crystals of the apoenzyme mixing of 0.001 ml enzyme solution containing 2 mM D-tert-Leu and 0.1 mM PLP with 0.001 ml of 0.5 M NaCl, 10 mM MgCl2, 10mM hexadecyltrimethylammonium bromide, for crystals of the PLP-L-Ile-bound enzyme, mixing of 0.001 ml protein solution with 0.001 ml of PLP-L-Ile, 20% PEG 3000, 0.2 M NaCl, 0.1 M HEPES, pH 7.5, and for crystals of the PLP-D-allo-Ile-bound enzyme are grown in sitting drops composed of 0.001 ml enzyme solution containing 1 mM PLP-D-allo-Ile mixed with an equal volume of 50 mM cadmium sulfate hydrate, 0.76 M sodium acetate trihydrate, and 0.1 M HEPES, pH 7.5. In all cases, drops are equilibrated against 0.1 ml mother liquor at 20°C, X-ray diffraction structure determination and analysis at resolutions of 2.77 A, 1.94 A, 2.65 A, and 2.12 A, respectively, molecular replacement using with the tetrameric structure of GABA-AT from Sulfolobus tokodaii (PDB ID 2eo5)
purified recombinant His-tagged enzyme alone or in complex with pyridoxal 5'-phosphate, hanging drop vapour diffusion technique, mixing of 0.002 ml of 2-8 mg/ml protein in 50 mM Na-phosphate, pH 7.2, and 0.1 mM 2-mercaptoethanol, with 0.002 ml of reservoir solution containing 12-18% PEG 3350 and 100 mM lithium citrate, 20°C, several weeks, for complex crystals soaking in pyridoxal 5'-phosphate containing mother liquor, X-ray diffraction structure determination and analysis at 2.6 A and 2.15 A resolution, respectively
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D222A
site-directed mutagenesis, the mutant shows reduced activity and altered kinetics compared to the wild-type enzyme
D222N
site-directed mutagenesis, the mutant shows reduced activity and altered kinetics compared to the wild-type enzyme
Y142F
site-directed mutagenesis, the mutant shows reduced activity and altered kinetics compared to the wild-type enzyme
additional information
additional information
generation of a T-DNA insertion mutant of gene daar1 leading to highly reduced levels of N-malonyl-D-allo-isoleucine
additional information
-
generation of a T-DNA insertion mutant of gene daar1 leading to highly reduced levels of N-malonyl-D-allo-isoleucine
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 11
the enzyme retains about 80% of its activity after incubation for 30 min
729935
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
30 min, the enzyme retains more than 80% of its activity
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged enzyme, rapid loss of activity at room temperature and when storing the enzyme at 4°C for overnight
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme DAAR1 from Escherichia coli strain Rosetta 2 pLysS by nickel affinity chromatography
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromtography and gel filtration
recombinant His/ProS2-tagged wild-type and mutant enzymes, tag cleavage
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene daar1, genotyping, untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana to establish genetic linkages between metabolites and genes, recombinant expression of His-tagged enzyme DAAR1 in Escherichia coli strain Rosetta 2 pLysS. The affinity tag does not affect enzyme activity or stability
recombinant expression of codon-optimized, His-tagged enzyme in Escherichia coli strain BL21(DE3)
sequence comparisons, recombinant expression of His/ProS2-tagged wild-type and mutant enzymes
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Mutaguchi, Y.; Ohmori, T.; Wakamatsu, T.; Doi, K.; Ohshima, T.
Identification, purification, and characterization of a novel amino acid racemase, isoleucine 2-epimerase, from Lactobacillus species
J. Bacteriol.
195
5207-5215
2013
Lentilactobacillus otakiensis, Lentilactobacillus buchneri (M1GRN3), Lentilactobacillus buchneri, Lentilactobacillus otakiensis JCM 15040, Lentilactobacillus buchneri JCM 1115 (M1GRN3)
brenda
Hayashi, J.; Mutaguchi, Y.; Minemura, Y.; Nakagawa, N.; Yoneda, K.; Ohmori, T.; Ohshima, T.; Sakuraba, H.
Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri
Acta Crystallogr. Sect. D
73
428-437
2017
Lentilactobacillus buchneri (M1GRN3), Lentilactobacillus buchneri
brenda
Awad, R.; Gans, P.; Reiser, J.B.
Structural insights into the substrate recognition and reaction specificity of the PLP-dependent fold-type I isoleucine 2-epimerase from Lactobacillus buchneri
Biochimie
137
165-173
2017
Lentilactobacillus buchneri (M1GRN3), Lentilactobacillus buchneri, Lentilactobacillus buchneri JCM 1115 (M1GRN3)
brenda
Strauch, R.C.; Svedin, E.; Dilkes, B.; Chapple, C.; Li, X.
Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
Proc. Natl. Acad. Sci. USA
112
11726-11731
2015
Arabidopsis thaliana (Q66GM9), Arabidopsis thaliana
brenda
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Release 2023.1 (January 2023)
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