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Enzyme Nomenclature
Information on EC 2.6.1.30 - pyridoxamine-pyruvate transaminase
for references in articles please use BRENDA:EC2.6.1.30
Word Map on EC 2.6.1.30
- 2.6.1.30
- pyridoxal
-
transamination
- 5'-phosphate
- 5'-deoxypyridoxal
- l-alanine
- nabh4
-
mesorhizobium
- loti
- analysis
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
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EC NUMBER 
COMMENTARY 
2.6.1.30
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RECOMMENDED NAME
GeneOntology No.
pyridoxamine-pyruvate transaminase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
pyridoxamine + pyruvate = pyridoxal + L-alanine
enzyme first binds pyridoxamine and then forms a Michaelis complex with the incoming pyruvate. The ketimine is formed through nucleophilic attack of the N-4' atom of pyridoxamine on the alpha-carbon atom of pyruvate, which is followed by the release of a water molecule. The stereospecific 1,3-prototropic shift between the ketimine and external aldimine via the quinonoid intermediate is accomplished through general base catalysis by Lys197. Pyridoxal and L-alanine are formed from the external aldimine and released from enzyme
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pyridoxamine + pyruvate = pyridoxal + L-alanine
enzyme first binds pyridoxamine and then forms a Michaelis complex with the incoming pyruvate. The ketimine is formed through nucleophilic attack of the N-4' atom of pyridoxamine on the alpha-carbon atom of pyruvate, which is followed by the release of a water molecule. The stereospecific 1,3-prototropic shift between the ketimine and external aldimine via the quinonoid intermediate is accomplished through general base catalysis by Lys197. Pyridoxal and L-alanine are formed from the external aldimine and released from enzyme
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pyridoxamine + pyruvate = pyridoxal + L-alanine
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
amino group transfer
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-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
pyridoxamine:pyruvate aminotransferase
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CAS REGISTRY NUMBER
COMMENTARY
9023-38-5
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Gram-negative bacillus isolate T2, 99.9% related to Ochrobactrum anthropi
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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
3-hydroxypyridine-4-aldehyde + L-alanine
3-hydroxy-4-aminomethylpyridine + pyruvate
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-
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r
omega-methylpyridoxal + L-alanine
omega-methylpyridoxamine + pyruvate
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i.e. 3-hydroxy-5-hydroxymethyl-2-ethylpyridine-4-carboxaldehyde
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r
pyridoxamine + 2-oxobutyrate
pyridoxal + (S)-2-aminobutyrate
poor substrate
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-
r
(S)-2-aminobutyrate + pyruvate
?
(S)-2-aminobutyrate is a poor substrate
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-
?
(S)-2-aminobutyrate + pyruvate
?
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(S)-2-aminobutyrate is a poor substrate
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?
pyridoxamine + pyruvate
pyridoxal + L-alanine
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oxaloacetate and several other keto acids tested cannot replace pyruvate as amino group acceptor
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r
pyridoxamine 5'-phosphate + pyruvate
pyridoxal 5'-phosphate + L-alanine
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-
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?
pyridoxamine 5'-phosphate + pyruvate
pyridoxal 5'-phosphate + L-alanine
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-
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?
additional information
?
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the enzyme shows less than 0.5% of the activity of pyridoxamine towards pyridoxamine 5'-phosphate (3.3 mM) with pyruvate as the amino acceptor, the enzyme shows less than 0.5% of the activity of pyruvate towards 2-oxoglutarate, 3-hydroxypyruvate, indol-pyruvate, phenylpyruvate, 3-methyl-2-oxobutyrate and 4-hydroxyphenylpyruvate when they are used at 10 mM
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additional information
?
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the enzyme shows less than 0.5% of the activity of pyridoxamine towards pyridoxamine 5'-phosphate (3.3 mM) with pyruvate as the amino acceptor, the enzyme shows less than 0.5% of the activity of pyruvate towards 2-oxoglutarate, 3-hydroxypyruvate, indol-pyruvate, phenylpyruvate, 3-methyl-2-oxobutyrate and 4-hydroxyphenylpyruvate when they are used at 10 mM
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additional information
?
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the enzyme shows less than 0.5% of the activity of pyridoxamine towards pyridoxamine 5'-phosphate (3.3 mM) with pyruvate as the amino acceptor, the enzyme shows less than 0.5% of the activity of pyruvate towards 2-oxoglutarate, 3-hydroxypyruvate, indol-pyruvate, phenylpyruvate, 3-methyl-2-oxobutyrate and 4-hydroxyphenylpyruvate when they are used at 10 mM
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additional information
?
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no substrate: oxaloacetate, hydroxypyruvate and phenylpyruvate
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additional information
?
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not active with: 3-deoxypyridoxal, pyridine-4-aldehyde, O-methylpyridoxal, 4-nitrosalicylaldehyde
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additional information
?
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temperature-jump and stopped-flow kinetic investigation of the rate and mechanism of the reaction of 5'-deoxy-pyridoxal with the enzyme
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additional information
?
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determination of the active site stoichiometry and the pH dependence of the dissociation constant for 5'-deoxypyridoxal
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additional information
?
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enzyme is part of the degradative pathway for vitamin B6 compounds utilized by Pseudomonas sp. MA-1
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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
additional information
?
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enzyme is part of the degradative pathway for vitamin B6 compounds utilized by Pseudomonas sp. MA-1
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pyridoxamine + pyruvate
pyridoxal + L-alanine
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oxaloacetate and several other keto acids tested cannot replace pyruvate as amino group acceptor
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r
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
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the bulky side chain of Glu68 interferes with the binding of the phosphate moiety of pyridoxal 5'-phosphate and makes the enzyme specific to pyridoxal
additional information
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pyridoxal 5'-phosphate is not required for activity
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4-Nitrosalicylaldehyde
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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
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hydroxylamine (10 mM), phenylhydrazine (1 mM) and sodium borohydride (1 mM) do not inactivate the enzyme
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additional information
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not inhibitory: hydroxylamine, phenylhydrazine and sodium borohydride
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Soil bacterium
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effect of pH on kinetic parameters
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4.6
2-oxoglutarate
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M2T/V70K/E212G mutant protein, pH 9.0, 30°C; V70K/E212G mutant protein, pH 9.0, 30°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
70
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at pH 9, 100 mM borate/KOH buffer; in 100 mM borate/KOH buffer pH 9.0
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
41000
41589
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4 * 41589, calculated from amino acid sequence; 4 * 41589, calculated from sequence
154000
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotetramer
homotetramer
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4 * 41000, SDS-PAGE; 4 * 41589, calculated from amino acid sequence
homotetramer
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4 * 41000, SDS-PAGE; 4 * 41589, calculated from amino acid sequence
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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
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addition of saturated ammonium sulfate solution to the concentrated protein solution until the first permanent turbidity appears, several days at 5°C
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30 - 80
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17% and 3% of the maximal activity is observed at 30°C and 80°C, respectively
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
loss of activity within 12 h at 25°C in sodium phosphate buffer, but is stable in potassium buffer under the same conditions
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
partial; partial, QA52 column chromatography and butyl-Toyopearl column chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli strains JM109 and BL21(DE3); expression in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
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
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low pyridoxamine 5'-phosphate:pyruvate aminotransferase activity, decrease in activity towards pyridoxamine
E68G
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low pyridoxamine 5'-phosphate:pyruvate aminotransferase activity, decrease in activity towards pyridoxamine
E68A
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low pyridoxamine 5'-phosphate:pyruvate aminotransferase activity, decrease in activity towards pyridoxamine
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E68G
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low pyridoxamine 5'-phosphate:pyruvate aminotransferase activity, decrease in activity towards pyridoxamine
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
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
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LINKS TO OTHER DATABASES (specific for EC-Number 2.6.1.30)
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