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Enzyme Nomenclature
Information on EC 5.1.1.1 - alanine racemase
for references in articles please use BRENDA:EC5.1.1.1
Word Map on EC 5.1.1.1
- 5.1.1.1
- pyridoxal
- 5'-phosphate
-
racemization
- peptidoglycan
- stearothermophilus
- d-cycloserine
-
plp-dependent
-
d-amino
-
aldimine
- d-alanyl-d-alanine
- exosporium
-
d-alanine:d-alanine
-
pyridoxal-5'-phosphate-dependent
-
5'-phosphate-dependent
-
quinonoid
- biotechnology
- drug development
- pharmacology
- medicine
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
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EC NUMBER 
COMMENTARY 
5.1.1.1
-
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RECOMMENDED NAME
GeneOntology No.
alanine racemase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-alanine = D-alanine
-
-
-
-
L-alanine = D-alanine
the active site of the alanine racemase reacts asymmetrically with the enantiomers of the substrate and has a conformation which greatly favors the D-enantiomer
-
L-alanine = D-alanine
the alanine racemase builds two different bases in the active site. The base for D-Ala may be closer to the enzyme surface, and that for L-Ala inside
-
L-alanine = D-alanine
consensus water sites at the interface between the two enzyme monomers maintain and stabilize dimer and supply the active site continuously with water molecules to allow rapid equilibration of active site protons
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
racemization
racemization
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
alanine racemase
A pyridoxal-phosphate protein.
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CAS REGISTRY NUMBER
COMMENTARY
9024-06-0
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
isolated from a urine specimen of a patient hospitalized in Busan, Republic of Korea, gene alr
-
-
isolated from a urine specimen of a patient hospitalized in Busan, Republic of Korea, gene alr
-
-
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2016, 2017, 2018, 2019, 2020, 2023, 2024, 2025, 2026, 2028, 2029, 2031, 2032, 2033, 2038, 650211, 651747, 652255, 652948, 662289, 674201, 987
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-
-
SwissProt
-
-
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
evolution
alanine racemase belongs to the fold-type III group of pyridoxal 5'-phosphate-dependent enzymes
evolution
-
the enzyme shows evolutionary and structural similarity to the promiscuous enzymes serine hydroxymethyltransferase, EC 2.1.2.1, and threonine aldolase, EC 4.1.2.48. The three enzymes represent a model of divergent evolution from an ancestral enzyme that was able to catalyse all the reactions of the modern enzymes. Similarly to serine hydroxymethyltransferase and threonine aldolase, Tolypocladium inflatum alanine racemase is able to catalyse retroaldol cleavage and transamination reactions
evolution
alanine racemase belongs to the fold-type III group of pyridoxal 5'-phosphate-dependent enzymes
evolution
-
alanine racemase belongs to the fold-type III group of pyridoxal 5'-phosphate-dependent enzymes
-
malfunction
during log phase growth without D-alanine, the viable counts of alanine racemase-deficient mutants of Burkholderia pseudomallei decrease within 2 h by about 10fold, and no viable bacteria are present at 24 h
malfunction
during log phase growth without D-alanine, the viable counts of alanine racemase-deficient mutants of Burkholderia pseudomallei decrease within 2 h by about 1000fold, and no viable bacteria are present at 24 h. The alanine racemase-deficient mutant of Burkholderia pseudomallei K96243 exhibits attenuation versus its isogenic parental strain with respect to growth and survival in murine peritoneal macrophages; during log phase growth without D-alanine, the viable counts of alanine racemase-deficient mutants of Burkholderia pseudomallei decrease within 2 h by about 1000fold, and no viable bacteria are present at 24 h. The alanine racemase-deficient mutant of Burkholderia pseudomallei K96243 exhibits attenuation versus its isogenic parental strain with respect to growth and survival in murine peritoneal macrophages
malfunction
because D-alanine is an essential component of the bacterial cell-wall peptidoglycan, inhibition of alanine racemase is lethal to prokaryotes
malfunction
-
depletion of D-alanine results in rapid loss of viability. The alr mutant is defective for growth in macrophages
malfunction
-
during log phase growth without D-alanine, the viable counts of alanine racemase-deficient mutants of Burkholderia pseudomallei decrease within 2 h by about 10fold, and no viable bacteria are present at 24 h
-
malfunction
-
during log phase growth without D-alanine, the viable counts of alanine racemase-deficient mutants of Burkholderia pseudomallei decrease within 2 h by about 1000fold, and no viable bacteria are present at 24 h. The alanine racemase-deficient mutant of Burkholderia pseudomallei K96243 exhibits attenuation versus its isogenic parental strain with respect to growth and survival in murine peritoneal macrophages; during log phase growth without D-alanine, the viable counts of alanine racemase-deficient mutants of Burkholderia pseudomallei decrease within 2 h by about 1000fold, and no viable bacteria are present at 24 h. The alanine racemase-deficient mutant of Burkholderia pseudomallei K96243 exhibits attenuation versus its isogenic parental strain with respect to growth and survival in murine peritoneal macrophages
-
malfunction
-
depletion of D-alanine results in rapid loss of viability. The alr mutant is defective for growth in macrophages
-
malfunction
-
because D-alanine is an essential component of the bacterial cell-wall peptidoglycan, inhibition of alanine racemase is lethal to prokaryotes
-
metabolism
-
biosynthesis of D-alanine as building blocks in the peptidoglycan layers of bacterial cell walls
physiological function
-
alanine racemase plays an essential role in cell wall synthesis as it racemizes L-alanine into D-alanine, a key building block in the biosynthesis of peptidoglycan
physiological function
-
alanine racemase catalyzes the racemization of L-alanine to D-alanine, which is a key component of the peptidoglycan layer, especially in cross-linking the bacterial cell walls
physiological function
-
the pyridoxal 5'-phosphate-dependent enzyme alanine racemase produces the D-alanine incorporated in the cyclic peptide cyclosporine A synthesized by the fungus
physiological function
-
involvement of alanine racemase in germination of Bacillus cereus spores lacking an intact exosporium. L-Alanine-mediated germination of food isolated Bacillus cereus DSA 1 spores, which lack an intact exosporium, is increased in the presence of D-cycloserine, an alanine racemase inhibitor, reflecting the activity of the Alr enzyme, capable of converting L-alanine to the germination inhibitor D-alanine, contribution of alanine racemase to the autoinhibition of Bacillus cereus spore germination
physiological function
-
the enzyme is essential for the organism, it is not possible to generate an alr knockout mutant in the absence of a complementing gene copy or D-alanine in the growth medium
physiological function
-
alanine racemase catalyzes the racemization of L-alanine to D-alanine, which is a key component of the peptidoglycan layer, especially in cross-linking the bacterial cell walls
-
physiological function
-
involvement of alanine racemase in germination of Bacillus cereus spores lacking an intact exosporium. L-Alanine-mediated germination of food isolated Bacillus cereus DSA 1 spores, which lack an intact exosporium, is increased in the presence of D-cycloserine, an alanine racemase inhibitor, reflecting the activity of the Alr enzyme, capable of converting L-alanine to the germination inhibitor D-alanine, contribution of alanine racemase to the autoinhibition of Bacillus cereus spore germination
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physiological function
-
the enzyme is essential for the organism, it is not possible to generate an alr knockout mutant in the absence of a complementing gene copy or D-alanine in the growth medium
-
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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
D-lysine
L-lysine
-
enzyme mutant I222T/Y354W, no activity with the wild-type enzyme
-
-
?
L-2-Aminobutyrate
D-2-Aminobutyrate
0.37% of the activity with L-Ala
-
r
L-2-aminobutyric acid
D-2-aminobutyric acid
-
18% of the activity with L-Ala
-
?
L-Arg
D-Arg
-
stepwise mechanism for alanine racemase at both 25°C and at 65°C. The carbanionic intermediate is obligatory, and Arg219 may serve to destabilize it to avoid side reactions such as transamination, a detailed reaction mechanism is proposed that includes enzyme and substrate protonation states
-
r
L-arginine
D-arginine
less than 10% activity compared to L-alanine
-
-
r
L-Methionine
D-Methionine
less than 10% activity compared to L-alanine
-
-
r
L-phenylalanine
D-phenylalanine
1.1% activity compared to L-alanine
-
-
r
L-proline
D-proline
1.1% activity compared to L-alanine
-
-
r
L-valine
D-valine
less than 10% activity compared to L-alanine
-
-
r
L-Ala
?
-
enzyme provides D-Ala as an essential building block for biosynthesis of the peptidoglycan layer of the cell wall
-
-
-
L-Ala
?
-
enzyme provides D-Ala as an essential building block for biosynthesis of the peptidoglycan layer of the cell wall
-
-
-
L-Ala
?
-
enzyme provides D-Ala as an essential building block for biosynthesis of the peptidoglycan layer of the cell wall
-
-
-
L-Ala
?
-
enzyme provides D-Ala as an essential building block for biosynthesis of the peptidoglycan layer of the cell wall
-
-
-
L-Ala
D-Ala
-
the enzyme catalyzes transamination as a side function.The pyridoxal form of the enzyme is converted to the pyridoxamine form by incubation with its natural substrate, D-alanine or L-alanine, under acidic conditions: the enzyme loses its racemase activity concomitantly. The pyridoxamine form of the enzyme returns to the pyridoxal form by incubation with pyruvate at alkaline pH
-
r
L-Ala
D-Ala
-
Tyr265 and Lys39 are the catalytic bases removing alpha-hydrogen from L- and D-alanine
-
r
L-Ala
D-Ala
-
the enzyme catalyzes the first committed step in bacterial cell wall biosynthesis
-
?
L-Ala
D-Ala
-
the ratio of the activity for conversion of D-alanine to L-alanine to that of the reverse conversion is constantly about 0.5 in the pH range 7-9.5
-
r
L-Ala
D-Ala
-
enzyme is required for production of D-Ala, a necessary component of the bacterial cell wall
-
?
L-alanine
D-alanine
-
enzyme provides D-Ala as a required compound for the synthesis of the peptidoglycan layer of the bacterial cell wall, Tolypocladium niveum requires alanine racemase for cyclosporin biosynthesis
-
r
L-alanine
D-alanine
-
alanine racemase can discriminate effectively between L-alanine and L-2-aminobutyric acid, and selectively and reversibly catalyzes L-alanine to D-alanine transformation Therefore, the enzyme shows ability of eliminating L-Ala from the reaction mixtures of L-2-aminobutyric acid biosynthesis, method optimization and evaluation in a coupled reaction with D-amino acid oxidase converting D-alanine to pyruvate stereoselectively, overview
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-
r
L-alanine
D-alanine
-
-
responsible for the synthesis of the d-alanine moiety present in cyclosporin A and of HC-toxin
-
-
L-alanine
D-alanine
TOXG encodes an alanine racemase whose function is to synthesize D-Ala for incorporation into HC-toxin, enzyme is involved in cyclic peptide biosynthesis
-
?
L-alanine
D-alanine
catalyzes the interconversion of D-alanine and L-alanine
-
-
r
L-alanine
D-alanine
catalyzes the interconversion of D-alanine and L-alanine, highly preferred substrate
-
-
r
L-alanine
D-alanine
-
first step in the biosynthesis of the peptidoglycan
-
-
?
L-alanine
D-alanine
-
The bacterium utilizes D-alanine (DAla) for synthesis of the peptidoglycan cell wall.
-
-
r
L-alanine
D-alanine
-
a major component of the alanine pathway, D-alanine is a major component in cell wall synthesis
-
-
?
L-alanine
D-alanine
catalyzes the interconversion of D-alanine and L-alanine
-
-
r
L-alanine
D-alanine
catalyzes the interconversion of D-alanine and L-alanine
-
-
r
L-alanine
D-alanine
-
responsible for the synthesis of the d-alanine moiety present in cyclosporin A and of HC-toxin
-
-
-
L-alanine
D-alanine
-
reversible reaction from an external aldimine in both directions via a quinonoid intermediate, overview
-
-
r
L-leucine
D-leucine
-
activity is 20% compared with L-alanine, other amino acids are not racemized
-
-
r
L-leucine
D-leucine
0.9% activity compared to L-alanine
-
-
r
L-lysine
D-lysine
less than 10% activity compared to L-alanine
-
-
r
L-lysine
D-lysine
-
enzyme mutant I222T/Y354W, no activity with the wild-type enzyme
-
-
?
L-serine
D-serine
less than 10% activity compared to L-alanine
-
-
r
additional information
?
-
-
exchange of the alpha-hydrogen of D-Ala and L-Ala with D2O
-
-
-
additional information
?
-
high specificity to L-alanine, low activity with L-arginine, L-methionine, L-lysine, L-serine, L-valine, L-proline, L-phenylalanine, L-leucine, respectively, no activity with L-histidine
-
-
-
additional information
?
-
-
the enzyme catalyzes transamination as side reaction, R-isomer preference in the hydrogen abstraction from pyridoxamine 5'-phosphate
-
?
additional information
?
-
-
the epsilon-amino group of Lys39 participates in both racemization and transamination when catalyzed by the wild-type enzyme
-
?
additional information
?
-
-
residues Ile222 and Tyr354 are important for the enzyme substrate specificity
-
-
-
additional information
?
-
-
no racemization of L-Ser, L-Asp, L-Glu, L-Val and L-Arg
-
?
additional information
?
-
-
the enzyme is only specific to L-alanine and L-isoleucine, and does not catalyze isomerization the other amino acids
-
-
-
additional information
?
-
-
the enzyme is only specific to L-alanine and L-isoleucine, and does not catalyze isomerization the other amino acids
-
-
-
additional information
?
-
-
alr racemase is constitutive and serves an anabolic function, dadB encoded enzyme is inducible and required for cell growth on L-Ala
-
-
-
additional information
?
-
-
alr racemase is constitutive and serves an anabolic function, dadB encoded enzyme is inducible and required for cell growth on L-Ala
-
-
-
additional information
?
-
-
two nonhomologous alanine racemase genes, one of which is associated with the catabolic function and the other of which presumably represents the biosynthetic function
-
-
-
additional information
?
-
-
key enzyme in cyclosporin A biosynthesis
-
-
-
additional information
?
-
-
Tolypocladium inflatum alanine racemase is able to catalyse retroaldol cleavage and transamination reactions, kinetic analysis and reaction mechanisms, overview
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
L-Ala
?
-
enzyme provides D-Ala as an essential building block for biosynthesis of the peptidoglycan layer of the cell wall
-
-
-
L-Ala
?
-
enzyme provides D-Ala as an essential building block for biosynthesis of the peptidoglycan layer of the cell wall
-
-
-
L-Ala
?
-
enzyme provides D-Ala as an essential building block for biosynthesis of the peptidoglycan layer of the cell wall
-
-
-
L-Ala
?
-
enzyme provides D-Ala as an essential building block for biosynthesis of the peptidoglycan layer of the cell wall
-
-
-
L-Ala
D-Ala
-
the enzyme catalyzes the first committed step in bacterial cell wall biosynthesis
-
?
L-Ala
D-Ala
-
enzyme is required for production of D-Ala, a necessary component of the bacterial cell wall
-
?
L-alanine
D-alanine
Q81VF6
-
enzyme provides D-Ala as a required compound for the synthesis of the peptidoglycan layer of the bacterial cell wall, Tolypocladium niveum requires alanine racemase for cyclosporin biosynthesis
-
r
L-alanine
D-alanine
-
-
responsible for the synthesis of the d-alanine moiety present in cyclosporin A and of HC-toxin
-
-
L-alanine
D-alanine
Q9UW18
TOXG encodes an alanine racemase whose function is to synthesize D-Ala for incorporation into HC-toxin, enzyme is involved in cyclic peptide biosynthesis
-
?
L-alanine
D-alanine
Q8R860
catalyzes the interconversion of D-alanine and L-alanine
-
-
r
L-alanine
D-alanine
-
first step in the biosynthesis of the peptidoglycan
-
-
?
L-alanine
D-alanine
-
The bacterium utilizes D-alanine (DAla) for synthesis of the peptidoglycan cell wall.
-
-
r
L-alanine
D-alanine
-
a major component of the alanine pathway, D-alanine is a major component in cell wall synthesis
-
-
?
L-alanine
D-alanine
Q04DI1
catalyzes the interconversion of D-alanine and L-alanine
-
-
r
L-alanine
D-alanine
Q04DI1
catalyzes the interconversion of D-alanine and L-alanine
-
-
r
L-alanine
D-alanine
-
responsible for the synthesis of the d-alanine moiety present in cyclosporin A and of HC-toxin
-
-
-
additional information
?
-
-
alr racemase is constitutive and serves an anabolic function, dadB encoded enzyme is inducible and required for cell growth on L-Ala
-
-
-
additional information
?
-
-
alr racemase is constitutive and serves an anabolic function, dadB encoded enzyme is inducible and required for cell growth on L-Ala
-
-
-
additional information
?
-
-
two nonhomologous alanine racemase genes, one of which is associated with the catabolic function and the other of which presumably represents the biosynthetic function
-
-
-
additional information
?
-
-
key enzyme in cyclosporin A biosynthesis
-
-
-
additional information
?
-
-
Tolypocladium inflatum alanine racemase is able to catalyse retroaldol cleavage and transamination reactions, kinetic analysis and reaction mechanisms, overview
-
-
-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FAD
-
not required as cofactor, slight activation at low concentrations, inhibition at high concentrations
pyridoxal 5'-phosphate
-
1 mol of pyridoxal 5'-phosphate is bound per subunit
pyridoxal 5'-phosphate
-
contains one mol of pyridoxal 5'-phosphate per mol of enzyme; Km: 0.000033 mM; the sequence of 10 amino acid residues around the Lys residue, to which pyridoxal 5'-phosphate is bound, is identical with that of the dadB racemase
pyridoxal 5'-phosphate
-
2 mol of pyridoxal 5'-phosphate bound per mol of enzyme dimer
pyridoxal 5'-phosphate
-
pyridoxal 5'-phosphate dependent enzyme
pyridoxal 5'-phosphate
-
pyridoxal 5'-phosphate dependent enzyme
pyridoxal 5'-phosphate
-
the monomeric inactive enzyme appears to bind the cofactor pyridoxal 5'-phosphate by a non-covalent linkage, although the native dimeric enzyme binds the cofactor through an aldimine Schiff base linkage
pyridoxal 5'-phosphate
-
2 mol of pyridoxal 5'-phosphate bound per mol of enzyme dimer
pyridoxal 5'-phosphate
-
pyridoxal 5'-phosphate binds to Lys of the enzyme protein and forms an aldimine Schiff base. The alpha-proton of the substrate is then abstracted, and the pyridoxal 5'-phosphate carbanion is generated; pyridoxal 5'-phosphate dependent enzyme
pyridoxal 5'-phosphate
-
pyridoxal 5'-phosphate binds to Lys of the enzyme protein and forms an aldimine Schiff base. The alpha-proton of the substrate is then abstracted, and the pyridoxal 5'-phosphate carbanion is generated; pyridoxal 5'-phosphate dependent enzyme
pyridoxal 5'-phosphate
-
pyridoxal 5'-phosphate binds to Lys of the enzyme protein and forms an aldimine Schiff base. The alpha-proton of the substrate is then abstracted, and the pyridoxal 5'-phosphate carbanion is generated; pyridoxal 5'-phosphate dependent enzyme
pyridoxal 5'-phosphate
-
pyridoxal 5'-phosphate binds to Lys of the enzyme protein and forms an aldimine Schiff base. The alpha-proton of the substrate is then abstracted, and the pyridoxal 5'-phosphate carbanion is generated; pyridoxal 5'-phosphate dependent enzyme
pyridoxal 5'-phosphate
-
not required as cofactor, slight activation at low concentrations, inhibition at high concentrations
pyridoxal 5'-phosphate
-
Arg219 forms a hydrogen bond with the pyridine nitrogen of the cofactor, Arg136 donates a hydrogen bond to the phenolic oxygen of pyridoxal 5'-phosphate and may be involved in the binding of substrate as well as stabilization of intermediates
pyridoxal 5'-phosphate
-
both active sites of the dimer contain a pyridoxal 5'-phosphate molecule in aldimine linkage to Lys39 as a protonated Schiff base. The protonated pyridoxal 5'-phosphate-Lys39 Schiff base is the reactive form of the enzyme
pyridoxal 5'-phosphate
-
each monomer is comprised of two domains, an eight-stranded alpha/beta barrel containing the pyridoxal 5'-phosphate cofactor and a second domain primarily composed of beta-strands. The cofactor adopts two partially occupied conformational states that resemble previously reported and external aldimine complexes
pyridoxal 5'-phosphate
-
enzyme is dependent on, maximal activity at 0.025 mM
pyridoxal 5'-phosphate
-
Km at 30°C is 0.005 mM. Maximal activity is obtained in presence of more than 0.125 mM pyridoxal 5'-phosphate. The decrease in activity at incubation temperatures over 40°C is consistent with the decrease in the amount of bound pyridoxal 5'-phosphate
pyridoxal 5'-phosphate
-
the pyridoxal form of the enzyme is converted to the pyridoxamine form by incubation with its natural substrate, D-alanine or L-alanine, under acidic conditions: the enzyme loses its racemase activity concomitantly. The pyridoxamine form of the enzyme returns to the pyridoxal form by incubation with pyruvate at alkaline pH
pyridoxal 5'-phosphate
-
C-terminal region of 1 subdomain: Arg138 donates a hydrogen bond to the phenolic O atom of PLP, Arg224 donates a hydrogen bond to the pyridinyl N atom of PLP, Lys41 forms an aldimine linkage with the PLP, eliminating water to form the Schiff base, C-terminal atoms of second subunit Ser209, Gly226 and Ile227 stabilize the PLP phosphate with the help of Ser209 O(gamma), Tyr45 O(eta) and Tyr359 O(eta)
pyridoxal 5'-phosphate
-
-
pyridoxal 5'-phosphate
-
stabilizes anionic intermediate after abstraction of alpha-hydrogen of the substrate amino acid by forming a quinoid intermediate
pyridoxal 5'-phosphate
-
stabilizes anionic intermediate after abstraction of alpha-hydrogen of the substrate amino acid by forming a quinoid intermediate
pyridoxal 5'-phosphate
-
once per 1 million turnovers of racemization a H-atom is added to C4-atom of the substrate moiety of the anionic intermediate instead of the reprotonation of the abstracted hydrogen at C(alpha) resulting in pyridoxamine 5'-phosphate
pyridoxal 5'-phosphate
-
stabilizes anionic intermediate after abstraction of alpha-hydrogen of the substrate amino acid by forming a quinoid intermediate
pyridoxal 5'-phosphate
-
PLP is inherently bound to the enzyme, removal of PLP inactivates the enzyme, adding PLP restores the activity, addition of 10 microM PLP to native enzyme slightly enhances activity
pyridoxal 5'-phosphate
PLP is bound to the enzyme, adding PLP during developement of enzyme or to an assay is not necessary
pyridoxal 5'-phosphate
dependent on, pyridoxal 5'-phosphate is bound to each monomer of the dimeric enzyme and forms a Schiff base with Lys39
pyridoxal 5'-phosphate
dependent on
pyridoxal 5'-phosphate
dependent on, alanine racemase requires pyridoxal-5'-phosphate as a cofactor to form a Schiff base between pyridoxal 5'-phosphate and epsilon-amino group of the lysine residue in the active site
additional information
-
contains a pyridoxal 5'-phosphate binding site
-
additional information
-
exogenous pyridoxal 5’-phosphate is not required, but enzyme may be pyridoxal 5’-phosphate-dependent
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1,1'-(2-oxido-1,2,5-oxadiazole-3,4-diyl)-bis (1-(2-thienyl))-methanone
-
-
2-(4,6-dimethyl-3-oxo-[1,2]thiazolo[5,4-b]pyridin-2-yl)-N-[2-(4-ethoxyphenyl)ethyl]acetamide
-
-
2-N',2-N',7-N',7-N'-tetramethyl-9H-fluorene-2,7-disulfonohydrazide
-
-
5-chloro-N-(3-chloro-4-methoxyphenyl)-2-(methylsulfonyl)pyrimidine-4-carboxamide
-
-
6-O-[3-chloro-4-(6-methoxycarbonylpyridine-2-carbonyl)oxyphenyl] 2-O-methyl pyridine-2,6-dicarboxylate
-
-
FAD
-
slight activation at low concentrations, inhibition at high concentrations
O-Carbamoyl-D-Ser
-
inhibition of wild type enzyme but not of the O-carbamoyl-D-Ser mutant
(R)-1-aminoethylphosphonic acid
-
in combination with pyridoxal 5'-phosphate
(R)-1-aminoethylphosphonic acid
-
upon formation of the external aldimine the phosphonate group interacts with putative catalytic residues, thereby rendering them unavailable for catalysis
beta,beta,beta-trifluoroalanine
-
nucleophilic attack of Lys38 on the electrophilic beta-difluoro-alpha,beta-unsaturated imine
beta,beta,beta-trifluoroalanine
-
nucleophilic attack of Lys38 on the electrophilic beta-difluoro-alpha,beta-unsaturated imine
cycloserine
-
8 microg/ml bacterial culture extract markedly inhibits alanine racemase
cycloserine
-
D-cycloserine or a racemic mixture of D- and L-cycloserine
D-cycloserine
-
time-dependent inactivation rate of enzyme from Streptomyces lavendulae is slower than for enzyme from Escherichia coli
D-cycloserine
-
model for inactivation mechanism via geminal diamine and ketimine to isoxazole
D-cycloserine
-
mechanism of inactivation and comparison with inactivation of Streptomyces lavendulae enzyme
D-cycloserine
-
specific inhibition is reversible by D-alanine in the growth medium
D-cycloserine
time-dependent inactivation rate of enzyme from Streptomyces lavendulae is slower than for enzyme from Escherichia coli. Enzyme from Streptomyces lavendulae is one of its self-resistance determinants
D-cycloserine
-
mechanism of inactivation and comparison with inactivation of Bacillus stearothermophilus enzyme
L-Cycloserine
-
model for inactivation mechanism via geminal diamine and ketimine to isoxazole
L-Cycloserine
-
mechanism of inactivation and comparison with inactivation of Streptomyces lavendulae enzyme
L-Cycloserine
-
mechanism of inactivation and comparison with inactivation of Bacillus stearothermophilus enzyme
propionate
-
propionate influences both Km (affinity for substrate) and Vmax (enzyme catalysis)
pyridoxal 5'-phosphate
-
slight activation at low concentrations, inhibition at high concentrations
Sodium borohydride
complete inactivation after dialysis against
Sodium borohydride
reduction of the enzyme by dialysis with sodium borohydride, the reduced enzyme is catalytically inactive and addition of pyridoxal 5'-phosphate does not reverse the inactivation
Sodium borohydride
reduction of the enzyme by dialysis with sodium borohydride, the reduced enzyme is catalytically inactive and addition of pyridoxal 5'-phosphate does not reverse the inactivation
Sodium borohydride
reduction of the enzyme by dialysis with sodium borohydride, the reduced enzyme is catalytically inactive and addition of pyridoxal 5'-phosphate does not reverse the inactivation
Sodium borohydride
reduction of the enzyme by dialysis with sodium borohydride, the reduced enzyme is catalytically inactive and addition of pyridoxal 5'-phosphate does not reverse the inactivation
additional information
the active-site binding pocket, dimer interface and active-site entryway of the enzyme are potential targets for structure-aided inhibitor design, formation of a template for structure-based drug-development efforts targeting the enzyme, overview
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
-
0.02 mM, activation to 108% of control in the direction of D-Ala formation, activation to 124% of control in the direction of L-Ala formation
additional information
-
activated in presence of monovalent anions including Cl-
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.304
D-alanine
-
+/-0.034, Alr P219A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
0.311
D-alanine
-
+/-0.008, Alr wildtype, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
0.402
D-alanine
-
+/-0.055, Alr E221K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
0.439
D-alanine
-
+/-0.080, Alr E221A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
0.513
D-alanine
-
+/-0.084, Alr E221P, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
0.528
D-alanine
-
+/-0.079, Alr E165K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
0.592
D-alanine
-
+/-0.085, Alr E165A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
0.604
D-alanine
-
+/-0.070, Alr D164K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
0.615
D-alanine
-
+/-0.032, Alr D164A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
0.89
D-alanine
pH not specified in the publication, 30°C, recombinant enzyme
1.008
D-alanine
-
+/-0.069, Alr wildtype, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
6.1
D-alanine
-
in 50 mM potassium phosphate buffer pH 7.4, at 30°C
20.16
D-alanine
pH 11.0, 70°C, recombinant enzyme
1.049
L-alanine
-
+/-0.131, Alr P219A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
1.401
L-alanine
-
+/-0.209, Alr E221P, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
1.516
L-alanine
-
+/-0.083, Alr E221A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
1.562
L-alanine
-
+/-0.256, Alr E165A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
1.993
L-alanine
-
+/-0.269, Alr E221K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
2.057
L-alanine
-
+/-0.038, Alr E165K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
2.77
L-alanine
pH not specified in the publication, 30°C, recombinant enzyme
3.03
L-alanine
-
+/-0.114, Alr D164A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
3.603
L-alanine
-
+/-0.180, Alr D164K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
9.3
L-alanine
-
in 50 mM potassium phosphate buffer pH 7.4, at 30°C
additional information
additional information
-
Km values of L-Ala in the presence of urea at various concentrations
-
additional information
additional information
-
Km values of L-Ala in the presence of urea at various concentrations
-
additional information
additional information
-
effect of NaCl on Km-value
-
additional information
additional information
-
Vmax for the racemization (D- to L-alanine and L- to D-alanine) is 87.0 and 84.8 U/mg, respectively.
-
additional information
additional information
-
Vmax 110 micromol/min/mg D-alanine; Vmax 323 micromol/min/mg L-alanine
-
additional information
additional information
-
Vmax 306 U/mg: D-alanine to L-alanine; Vmax 345 U/mg: L-alanine to D-alanine
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.333
D-alanine
-
+/-0.033, Alr D164K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
1.317
D-alanine
-
+/-0.100, Alr E165K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
4
D-alanine
-
+/-0.417, Alr E165A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
4.466
D-alanine
-
+/-0.200, Alr D164A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
5.267
D-alanine
-
+/-0.333, Alr P219A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
5.783
D-alanine
-
+/-0.483, Alr wildtype, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
6.35
D-alanine
-
+/-0.333, Alr E221K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
6.817
D-alanine
-
+/-0.650, Alr E221A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
7.617
D-alanine
-
+/-0.750, Alr E221P, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
2.8
L-alanine
-
+/-0.250, Alr D164K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
16.72
L-alanine
-
+/-0.850, Alr E165K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
22.47
L-alanine
-
+/-2.667, Alr E165A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
41.82
L-alanine
-
+/-2.600, Alr D164A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
51.77
L-alanine
-
+/-6.067, Alr P219A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
53.98
L-alanine
-
+/-3.217, Alr wildtype, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
67.07
L-alanine
-
+/-7.633, Alr E221P, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
68.23
L-alanine
-
+/-7.550, Alr E221K, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
70.92
L-alanine
-
+/-2.333, Alr E221A, 30°C, pH 8.0, spectrophotometrically measured at 340 nm
1133
L-alanine
-
pH 8.0, 30°C, recombinant mutant I222T/Y354W; pH 8.0, 30°C, recombinant mutant Y354W
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
158.3
D-alanine
-
pH 8.0, 30°C, recombinant mutant I222T/Y354W
136.7
L-alanine
-
pH 8.0, 30°C, recombinant mutant I222T/Y354W
300
L-alanine
-
pH 8.0, 30°C, recombinant mutant I222T; pH 8.0, 30°C, recombinant wild-type enzyme
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.086
(4R)-4-amino-3-isoxazolidinone
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.93
2-(4,6-dimethyl-3-oxo-[1,2]thiazolo[5,4-b]pyridin-2-yl)-N-[2-(4-ethoxyphenyl)ethyl]acetamide
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.08
2-phenyl-1-piperidin-1-ylethanethione
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.02
3,3-dihydroxy-1H-quinoline-2,4-dione
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.76
5-chloro-N-(3-chloro-4-methoxyphenyl)-2-(methylsulfonyl)pyrimidine-4-carboxamide
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.68
6-O-[3-chloro-4-(6-methoxycarbonylpyridine-2-carbonyl)oxyphenyl] 2-O-methyl pyridine-2,6-dicarboxylate
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.038
ethyl 3-(pyridin-2-ylthio)propanoate
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.63
N-benzyl-5-chloro-2-methylsulfonylpyrimidine-4-carboxamide
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.058
(4R)-4-amino-3-isoxazolidinone
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0049
1,1'-(2-oxido-1,2,5-oxadiazole-3,4-diyl)-bis (1-(2-thienyl))-methanone
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0057
2-(2-hydroxyphenoxy)-N-methylacetamide
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0077
2-(4,6-dimethyl-3-oxo-[1,2]thiazolo[5,4-b]pyridin-2-yl)-N-[2-(4-ethoxyphenyl)ethyl]acetamide
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0033
2-(4-methoxyphenyl)-1-morpholin-4-ylethanethione
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0065
2-(4-methylphenyl)-1-morpholin-4-ylethanethione
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0028
2-(hydoxyimino)-6-methyl-2H-benzopyran-3-carboxamide
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0131
2-(pyridin-3-ylcarbamothioyl sulfanyl)acetic acid
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0016
2-N',2-N',7-N',7-N'-tetramethyl-9H-fluorene-2,7-disulfonohydrazide
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.006
2-phenyl-1-piperidin-1-ylethanethione
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0052
3,3-dihydroxy-1H-quinoline-2,4-dione
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0082
5-chloro-N-(3-chloro-4-methoxyphenyl)-2-(methylsulfonyl)pyrimidine-4-carboxamide
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.001
6-O-[3-chloro-4-(6-methoxycarbonylpyridine-2-carbonyl)oxyphenyl] 2-O-methyl pyridine-2,6-dicarboxylate
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0026
ethyl 3-(pyridin-2-ylthio)propanoate
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.009
N',N',4-trimethylbenzenesulfonohydrazide
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0068
N-benzyl-5-chloro-2-methylsulfonylpyrimidine-4-carboxamide
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.0082
N-hydroxy-2-(2-hydroxyphenoxy)acetamide
Mycobacterium tuberculosis
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
16.5
-
after 3.7fold purification, using L-isoleucine as substrate, at pH 9.0 and 37°C
42.6
-
after 3.7fold purification, using L-alanine as substrate, at pH 9.0 and 37°C
1414
purified recombinant wild-type enzyme, pH 11.0, 70°C
additional information
additional information
-
Vmax of racemization of L- to D-alanine is 101 micromol/min/mg
additional information
-
assay method based on circular dichroism spectra of D- and L-alanine
additional information
-
assay method based on circular dichroism spectra of D- and L-alanine
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.3
8.5
9.5
10 - 10.5
yncD, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
10
9.5
dal, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 11
7 - 9.5
-
7.0: about 45% of maximal activity, 9.5: about 95% of maximal activity
7.5 - 12.5
-
at pH 7.5 and at pH 12.5 activity is just under 40%, at pH 7 and at pH 13 the enzyme is inactive
8.5 - 11
9 - 11
-
pH 9: about 50% of maximal activity, pH 11.0: about 35% of maximal activity, racemization from D-Ala to L-Ala
7 - 11
-
pH 7.0: about 75% of maximal activity, pH 11.0: about 75% of maximal activity
7 - 11
-
pH 7.0: about 40% of maximal activity in formation of D-Ala, about 50% of maximal activity in formation of L-Ala, pH 11: about 95% of maximal activity in formation of L-Ala and D-Ala
8.5 - 11
pH 8.5: 35% of max. activity, pH 11: 8% of max. activity, dal, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase; pH 8.5: 42% of max. activity, pH 11: 58% of max. activity, yncD, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
8.5 - 11
-
pH 8.5: about 55% of maximal activity, pH 11.0: about 65% of maximal activity, racemization from L-Ala to D-Ala
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
37
40
50
55
yncD, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
60
additional information
-
no temperature dependency of the enzyme is observed with D-Ala
50
dal, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
60
in presence of an excess amount of pyridoxal 5'-phosphate, 0.4 mM
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0 - 70
-
between 20 to 50°C the enzyme activity is 75-100%, at 0°C activity is about 28% and at 70°C activity is 20%
0 - 60
about 30% of maximal activity at 0°C and at 60°C, in absence of pyridoxal 5'-phosphate
0 - 40
-
0°C: about 25% of maximal activity, 40°C: about 45% of maximal activity
20 - 50
-
20°C: about 60% of maximal activity, 50°C, about 35% of maximal activity
25 - 50
30 - 50
30°C, 45% of maximal activity, 50°C: about 50% of maximal activity, in presence of an excess amount of pyridoxal 5'-phosphate, 0.4 mM
30 - 60
30°C and 60°C: approx. 20% of max. activity, dal, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
30 - 70
30°C: approx. 25% of max. activity, 70°C: approx. 8% of max. activity, yncD, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
35 - 100
-
35°C: about 75% of maximal activity, 100°C: about 55% of maximal activity
40 - 70
-
40°C: about 60% of maximal activity, 70°C: about 50% of maximal activity
25 - 50
-
25°C: about 65% of maximal activity, formation of L-Ala or D-Ala, 50°C: about 50% of maximal activity in formation of D-Ala, about 60% of maximal activity in formation of L-Ala
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Actinobacillus succinogenes (strain ATCC 55618 / 130Z)
Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240)
Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240)
Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1)
Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Enterococcus faecalis (strain ATCC 700802 / V583)
Enterococcus faecalis (strain ATCC 700802 / V583)