Information on EC 5.1.1.1 - alanine racemase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea

EC NUMBER
COMMENTARY hide
5.1.1.1
-
RECOMMENDED NAME
GeneOntology No.
alanine racemase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-alanine = D-alanine
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
-
stereoisomerization
racemization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
alanine metabolism
-
-
anaerobic energy metabolism (invertebrates, cytosol)
-
-
D-Alanine metabolism
-
-
L-alanine biosynthesis I
-
-
L-alanine degradation I
-
-
Metabolic pathways
-
-
SYSTEMATIC NAME
IUBMB Comments
alanine racemase
A pyridoxal-phosphate protein.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-06-0
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
Uniprot
Manually annotated by BRENDA team
13H
-
-
Manually annotated by BRENDA team
isolated from a urine specimen of a patient hospitalized in Busan, Republic of Korea, gene alr
-
-
Manually annotated by BRENDA team
isolated from a urine specimen of a patient hospitalized in Busan, Republic of Korea, gene alr
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
motile strain isolated from gnocchi
-
-
Manually annotated by BRENDA team
motile strain isolated from gnocchi
-
-
Manually annotated by BRENDA team
strain OF4
TREMBL
Manually annotated by BRENDA team
strain OF4
TREMBL
Manually annotated by BRENDA team
strain YM-1
-
-
Manually annotated by BRENDA team
strain YM-1
-
-
Manually annotated by BRENDA team
strain 168
SwissProt
Manually annotated by BRENDA team
subsp. Kurstaki
SwissProt
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
L.
-
-
Manually annotated by BRENDA team
L.
-
-
Manually annotated by BRENDA team
no activity in Bacillus subtilis
strain DN1686, D-Ala auxotrophic mutant
-
-
Manually annotated by BRENDA team
no activity in Bacillus subtilis DN1686
strain DN1686, D-Ala auxotrophic mutant
-
-
Manually annotated by BRENDA team
locus OEOE_1641, strain ATCC BAA-331/PSU-1
UniProt
Manually annotated by BRENDA team
locus OEOE_1641, strain ATCC BAA-331/PSU-1
UniProt
Manually annotated by BRENDA team
strain A237
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
overproducing strain
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Thalassiosira sp.
culture under germ-free conditions
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-Ala
L-Ala
show the reaction diagram
-
-
-
-
r
D-alanine
L-alanine
show the reaction diagram
D-lysine
L-lysine
show the reaction diagram
-
enzyme mutant I222T/Y354W, no activity with the wild-type enzyme
-
-
?
D-serine
L-serine
show the reaction diagram
-
-
-
-
r
L-2-Aminobutyrate
D-2-Aminobutyrate
show the reaction diagram
0.37% of the activity with L-Ala
-
r
L-2-aminobutyric acid
D-2-aminobutyric acid
show the reaction diagram
-
18% of the activity with L-Ala
-
?
L-Ala
?
show the reaction diagram
L-Ala
D-Ala
show the reaction diagram
L-alanine
D-alanine
show the reaction diagram
L-alanine
R-alanine
show the reaction diagram
-
-
-
r
L-Arg
D-Arg
show the reaction diagram
-
stepwise mechanism for alanine racemase at both 25C and at 65C. 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
show the reaction diagram
less than 10% activity compared to L-alanine
-
-
r
L-isoleucine
D-isoleucine
show the reaction diagram
L-leucine
D-leucine
show the reaction diagram
L-lysine
D-lysine
show the reaction diagram
L-Methionine
D-Methionine
show the reaction diagram
less than 10% activity compared to L-alanine
-
-
r
L-phenylalanine
D-phenylalanine
show the reaction diagram
1.1% activity compared to L-alanine
-
-
r
L-proline
D-proline
show the reaction diagram
1.1% activity compared to L-alanine
-
-
r
L-Ser
D-Ser
show the reaction diagram
L-serine
D-serine
show the reaction diagram
L-valine
D-valine
show the reaction diagram
less than 10% activity compared to L-alanine
-
-
r
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
D-alanine
L-alanine
show the reaction diagram
L-Ala
?
show the reaction diagram
L-Ala
D-Ala
show the reaction diagram
L-alanine
D-alanine
show the reaction diagram
L-alanine
R-alanine
show the reaction diagram
P0A6B4
-
-
-
r
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
FAD
-
not required as cofactor, slight activation at low concentrations, inhibition at high concentrations
pyridoxal 5'-phosphate
additional information
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
slight activation at 1 mM
Co2+
-
120% activity at 1 mM
Fe2+
-
slight activation at 1 mM
Mg2+
-
slight activation at 1 mM
Mn2+
-
130% activity at 1 mM
Ni2+
-
slight activation at 1 mM
Sr2+
-
158% activity at 1 mM
additional information
-
not influenced by 1 mM Zn2+ or Sn2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(1-Aminoethyl)boronic acid
-
-
(1-Aminoethyl)phosphonate
(4R)-4-amino-3-isoxazolidinone
-
-
(R)-1-aminoethylphosphonic acid
1,1'-(2-oxido-1,2,5-oxadiazole-3,4-diyl)-bis (1-(2-thienyl))-methanone
-
-
1-amino-cyclopropane phosphonate
-
-
2-(2-hydroxyphenoxy)-N-methylacetamide
-
-
2-(4,6-dimethyl-3-oxo-[1,2]thiazolo[5,4-b]pyridin-2-yl)-N-[2-(4-ethoxyphenyl)ethyl]acetamide
-
-
2-(4-methoxyphenyl)-1-morpholin-4-ylethanethione
-
-
2-(4-methylphenyl)-1-morpholin-4-ylethanethione
-
-
2-(hydoxyimino)-6-methyl-2H-benzopyran-3-carboxamide
-
-
2-(pyridin-3-ylcarbamothioyl sulfanyl)acetic acid
-
-
2-Amino-3-chlorobut-3-enoic acid
2-Amino-3-fluorobut-3-enoic acid
2-N',2-N',7-N',7-N'-tetramethyl-9H-fluorene-2,7-disulfonohydrazide
-
-
2-phenyl-1-piperidin-1-ylethanethione
-
-
3,3-dihydroxy-1H-quinoline-2,4-dione
-
-
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
-
-
alanine phosphonate
-
-
Aminooxyacetate
-
1 mM, complete inhibition, both directions
aminooxyacetic acid
beta,beta,beta-trifluoroalanine
beta-chloroalanine
-
-
beta-fluoroalanine
-
-
chloro-vinyl glycine
-
-
Cu2+
-
40% residual activity at 1 mM
cycloserine
D-Chloroalanine
D-cycloserine
D-penicillamine
-
1 mM, 79% inhibition
ethyl 3-(pyridin-2-ylthio)propanoate
-
-
FAD
-
slight activation at low concentrations, inhibition at high concentrations
fluoro-alanine
-
-
fluoro-vinyl glycine
-
-
hydroxylamine
L-alanine phosphonic acid
-
-
L-chloroalanine
L-Cycloserine
L-Penicillamine
-
1 mM, 28% inhibition
N',N',4-trimethylbenzenesulfonohydrazide
-
-
N-benzyl-5-chloro-2-methylsulfonylpyrimidine-4-carboxamide
-
-
N-hydroxy-2-(2-hydroxyphenoxy)acetamide
-
-
NaBH4
-
0.5 M, loss of activity
NEM
-
1 mM, 22% inhibition
O-Carbamoyl-D-Ser
-
inhibition of wild type enzyme but not of the O-carbamoyl-D-Ser mutant
O-carbamoyl-D-serine
-
-
PCMB
-
1 mM, 91% inhibition
phenylhydrazine
Propionate
pyridoxal 5'-phosphate
pyruvate
-
-
Sodium borohydride
Vinylglycine
-
-
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
DTT
-
optimal activation at 40 mM
glutathione
-
required for maximal activity
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-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.4 - 179
D-Ala
0.25 - 20.4
D-alanine
18
D-Lysine
-
pH 8.0, 30C, recombinant mutant I222T/Y354W
10
D-serine
-
pH 8.2, 37C
0.5 - 171
L-Ala
0.29 - 100
L-alanine
32
L-lysine
-
pH 8.0, 30C, recombinant mutant I222T/Y354W
27
L-serine
-
pH 8.2, 37C
additional information
additional information
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.6 - 3272
D-Ala
0.06 - 1017
D-alanine
2.5
D-Lysine
Geobacillus stearothermophilus
-
pH 8.0, 30C, recombinant mutant I222T/Y354W
5.5
D-serine
Streptomyces lavendulae
-
pH 8.2, 37C
1.1 - 7504
L-Ala
0.9 - 1533
L-alanine
4.17
L-lysine
Geobacillus stearothermophilus
-
pH 8.0, 30C, recombinant mutant I222T/Y354W
13.3
L-serine
Streptomyces lavendulae
-
pH 8.2, 37C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.045 - 383.3
D-alanine
0.14
D-Lysine
Geobacillus stearothermophilus
-
pH 8.0, 30C, recombinant mutant I222T/Y354W
1531
0.038 - 300
L-alanine
0.13
L-lysine
Geobacillus stearothermophilus
-
pH 8.0, 30C, recombinant mutant I222T/Y354W
134
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
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
0.33 - 4
D-cycloserine
0.038
ethyl 3-(pyridin-2-ylthio)propanoate
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
0.16
hydroxylamine
-
-
6 - 8.2
L-Cycloserine
0.63
N-benzyl-5-chloro-2-methylsulfonylpyrimidine-4-carboxamide
-
in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication
20 - 30
Propionate
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
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
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
11.5
-
crude extract, using L-alanine as substrate, at pH 9.0 and 37C
16.5
-
after 3.7fold purification, using L-isoleucine as substrate, at pH 9.0 and 37C
42.6
-
after 3.7fold purification, using L-alanine as substrate, at pH 9.0 and 37C
61.8
in presence of 50 mM L-alanine with a 5.0% yield
295
-
at 37C
1414
purified recombinant wild-type enzyme, pH 11.0, 70C
3708
-
substrate is D-alanine
10500
-
substrate is L-alanine
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
-
assay at
10 - 10.5
yncD, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
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
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35
in absence of pyridoxal 5'-phosphate
35 - 40
-
-
55
yncD, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
additional information
-
no temperature dependency of the enzyme is observed with D-Ala
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0 - 70
-
between 20 to 50C the enzyme activity is 75-100%, at 0C activity is about 28% and at 70C activity is 20%
0 - 60
about 30% of maximal activity at 0C and at 60C, in absence of pyridoxal 5'-phosphate
0 - 40
-
0C: about 25% of maximal activity, 40C: about 45% of maximal activity
20 - 50
-
20C: about 60% of maximal activity, 50C, about 35% of maximal activity
25 - 50
30 - 50
30C, 45% of maximal activity, 50C: about 50% of maximal activity, in presence of an excess amount of pyridoxal 5'-phosphate, 0.4 mM
30 - 60
30C and 60C: approx. 20% of max. activity, dal, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
30 - 70
30C: approx. 25% of max. activity, 70C: approx. 8% of max. activity, yncD, extracts are assayed (in triplicate) by monitoring NADH production in spectrophotometric assay with L-alanine dehydrogenase
35 - 100
-
35C: about 75% of maximal activity, 100C: about 55% of maximal activity
40 - 70
-
40C: about 60% of maximal activity, 70C: about 50% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.2
-
isoelectric focusing
6.5
calculation from nucleotide sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Oenococcus oeni (strain ATCC BAA-331 / PSU-1)
Oenococcus oeni (strain ATCC BAA-331 / PSU-1)
Peptoclostridium difficile (strain 630)
Peptoclostridium difficile (strain 630)
Peptoclostridium difficile (strain 630)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Staphylococcus aureus (strain COL)
Staphylococcus aureus (strain Mu50 / ATCC 700699)
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)