Information on EC 2.6.1.30 - pyridoxamine-pyruvate transaminase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
2.6.1.30
-
RECOMMENDED NAME
GeneOntology No.
pyridoxamine-pyruvate transaminase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
pyridoxamine + pyruvate = pyridoxal + L-alanine
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
amino group transfer
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-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
vitamin B6 degradation
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-
Vitamin B6 metabolism
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Microbial metabolism in diverse environments
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SYSTEMATIC NAME
IUBMB Comments
pyridoxamine:pyruvate aminotransferase
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CAS REGISTRY NUMBER
COMMENTARY hide
9023-38-5
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Gram-negative bacillus isolate T2, 99.9% related to Ochrobactrum anthropi
-
-
Manually annotated by BRENDA team
strain MA-1
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-
Manually annotated by BRENDA team
Soil bacterium
-
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(S)-2-aminobutyrate + pyruvate
?
show the reaction diagram
(S)-2-aminobutyrate is a poor substrate
-
-
?
2-norpyridoxal + L-alanine
2-norpyridoxamine + pyruvate
show the reaction diagram
3-hydroxypyridine-4-aldehyde + L-alanine
3-hydroxy-4-aminomethylpyridine + pyruvate
show the reaction diagram
-
-
-
r
5-deoxypyridoxal + L-alanine
5-deoxypyridoxamine + pyruvate
show the reaction diagram
omega-methylpyridoxal + L-alanine
omega-methylpyridoxamine + pyruvate
show the reaction diagram
pyridoxamine + 2-oxobutyrate
?
show the reaction diagram
-
-
-
?
pyridoxamine + 2-oxobutyrate
pyridoxal + (S)-2-aminobutyrate
show the reaction diagram
poor substrate
-
-
r
pyridoxamine + 2-oxoglutarate
pyridoxal + L-glutamate
show the reaction diagram
-
-
-
-
r
pyridoxamine + pyruvate
pyridoxal + L-alanine
show the reaction diagram
pyridoxamine 5'-phosphate + pyruvate
pyridoxal 5'-phosphate + L-alanine
show the reaction diagram
-
-
-
?
additional information
?
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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
pyridoxamine + pyruvate
pyridoxal + L-alanine
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
-
activates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-Deoxypyridoxal
-
inhibits pyridoxamine formation from pyridoxal + alanine
4-Nitrosalicylaldehyde
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inhibits pyridoxamine formation from pyridoxal + alanine
N-Methylpyridoxal
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inhibits pyridoxamine formation from pyridoxal + alanine
O-Methylpyridoxal
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inhibits pyridoxamine formation from pyridoxal + alanine
Pyridine-4-aldehyde
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inhibits pyridoxamine formation from pyridoxal + alanine
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
phosphate is neither essential nor inhibitory
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
20
(S)-2-aminobutyrate
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; 30C, pH 9.0
0.59
2-norpyridoxal
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pH 8.9, 25C
0.16
2-Norpyridoxamine
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pH 8.9, 25C
7.1
2-oxobutyrate
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; 30C, pH 9.0
8.8 - 110.3
2-oxoglutarate
0.89
3-hydroxypyridine-4-aldehyde
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pH 8.9, 25C
0.009
5-Deoxypyridoxal
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pH 8.9, 25C
0.014
5-Deoxypyridoxamine
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pH 8.9, 25C
0.58 - 64.5
L-alanine
29.3 - 142
L-glutamate
1.3
omega-methylpyridoxal
-
pH 8.9, 25C
0.012 - 0.059
pyridoxal
0.013 - 2.5
pyridoxamine
3.4
pyridoxamine 5'-phosphate
mutant E68A, pH 9.0, 30C
0.1 - 7.4
pyruvate
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
9
(S)-2-aminobutyrate
Mesorhizobium loti
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; 30C, pH 9.0
24
2-oxobutyrate
Mesorhizobium loti
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; 30C, pH 9.0
1.9 - 9.1
2-oxoglutarate
41
L-alanine
Mesorhizobium loti
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; 30C, pH 9.0
1.5 - 6.4
L-glutamate
41
pyridoxal
Mesorhizobium loti
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; 30C, pH 9.0
0.77 - 8
pyridoxamine
0.062 - 0.22
pyridoxamine 5'-phosphate
29
pyruvate
Mesorhizobium loti
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; 30C, pH 9.0
additional information
additional information
Pseudomonas sp.
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-
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.023 - 0.916
2-oxoglutarate
34
0.012 - 0.152
L-glutamate
41
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.00631
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at 30C
7.3
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purified enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
9.5
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estimated based on the Km and kcat values
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 10
Soil bacterium
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-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
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assay at
37
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assay at
70
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at pH 9, 100 mM borate/KOH buffer; in 100 mM borate/KOH buffer pH 9.0
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 80
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30: 17% of maximal activity, 80C: 3% of maximal activity
PDB
SCOP
CATH
ORGANISM
UNIPROT
Rhizobium loti (strain MAFF303099)
Rhizobium loti (strain MAFF303099)
Rhizobium loti (strain MAFF303099)
Rhizobium loti (strain MAFF303099)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
154000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
tetramer
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4 * 41000, SDS-PAGE; 4 * 41589, calculated from sequence
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
native enzyme, space group P43212, diffraction to 2.0 A resolution. Complexes with pyridoxamine, pyridoxal, and pyridoxyl-L-alanine at 1.7 A, 1.7 A, and 2.0 A resolution, respectively. Enzyme is a homotetramer and each subunit is composed of a large N-terminal domain, consisting of seven beta-sheets and eight alpha-helices, and a smaller C-terminal domain, consisting of three beta-sheets and four alpha-helices. The substrate pyridoxal is bound through an aldimine linkage to Lys197 in the active site. The carboxylate group of the substrate amino/keto acid is hydrogen-bonded to Arg336 and Arg345
addition of saturated ammonium sulfate solution to the concentrated protein solution until the first permanent turbidity appears, several days at 5C
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 80
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17% and 3% of the maximal activity is observed at 30C and 80C, respectively
70
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10 min, stable
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
K+ stabilizes
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
loss of activity within 12 h at 25C in sodium phosphate buffer, but is stable in potassium buffer under the same conditions
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hydrophobic interaction chromatography, gel filtration
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partial; partial, QA52 column chromatography and butyl-Toyopearl column chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3)
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expressed in Escherichia coli strains JM109 and BL21(DE3); expression in Escherichia coli
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expression in Escherichia coli
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C198A
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enzyme shows the same specific activity as that of the wild type enzyme; shows activity of the wild type enzyme
E68A
low pyridoxamine 5'-phosphate:pyruvate aminotransferase activity, decrease in activity towards pyridoxamine
E68G
low pyridoxamine 5'-phosphate:pyruvate aminotransferase activity, decrease in activity towards pyridoxamine
K197L
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mutant enzyme shows no activity; shows no activity
M2T/V70K
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M2: surface residue
M2T/V70K/E212G
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E212: surface residue
M2T/Y35H/V70K
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Y35: active site residur
M2T/Y35H/V70K/E212G
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E212: surface residue
R336A
significant decrease in affinity for pyruvate
V70K
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active site residue, increase in reactivity toward 2-oxoglutarate
V70K/E212G
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E212: surface residue
V70R
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active site residue, elimination of activity
V70R/F247C
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F247: hydrophobic core residue
Y35H/V70K
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active site residues
Y35H/V70R/F247C
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F247: hydrophobic core residue
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
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determination method for individual natural vitamin B6 compounds. Compounds are specifically converted into 4-pyridoxolactone by pyridoxal 4-dehydrogenase and coupling reactions involving pyridoxine 4-oxidase, pyridoxal 4-dehydrogenase, or pyridoxamine-pyruvate aminotransferase and pyridoxal 4-dehydrogenase. Application of method for analysis of food samples