Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary extracted from

  • Holland, C.K.; Berkovich, D.A.; Kohn, M.L.; Maeda, H.; Jez, J.M.
    Structural basis for substrate recognition and inhibition of prephenate aminotransferase from Arabidopsis (2018), Plant J., 94, 304-314 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.6.1.1 AtPAT wild-type enzyme and K306A, T84V, and T84V/K169V mutant enzymes in complex with either 2-oxoglutarate or pyridoxamine 5'-phosphate and glutamate, X-ray diffraction structure determination and analysis at 1.4-3.0 A resolution, molecular replacement Arabidopsis thaliana
2.6.1.78 AtPAT wild-type enzyme and K306A, T84V, and T84V/K169V mutant enzymes in complex with either 2-oxoglutarate or pyridoxamine 5'-phosphate and glutamate, X-ray diffraction structure determination and analysis at 1.4-3.0 A resolution, molecular replacement Arabidopsis thaliana
2.6.1.79 AtPAT wild-type enzyme and K306A, T84V, and T84V/K169V mutant enzymes in complex with either 2-oxoglutarate or pyridoxamine 5'-phosphate and glutamate, X-ray diffraction structure determination and analysis at 1.4-3.0 A resolution, molecular replacement Arabidopsis thaliana

Protein Variants

EC Number Protein Variants Comment Organism
2.6.1.1 A168G site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.1 E108K site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.1 K169S site-directed mutagenesis, inactive with aspartate and glutamate Arabidopsis thaliana
2.6.1.1 K169V site-directed mutagenesis, inactive with glutamate, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.1 K306A site-directed mutagenesis, structure comparison with wild-type, overview. The alanine substitution of Lys306 prevents Schiff base formation with the cofactor, inactive mutant Arabidopsis thaliana
2.6.1.1 R445G site-directed mutagenesis, inactive mutant Arabidopsis thaliana
2.6.1.1 T84V site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.1 T84V/K169V site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.78 A168G site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.78 E108K site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.78 K169S site-directed mutagenesis, inactive with aspartate and glutamate Arabidopsis thaliana
2.6.1.78 K169V site-directed mutagenesis, inactive with glutamate, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.78 K306A site-directed mutagenesis, structure comparison with wild-type, overview. The alanine substitution of Lys306 prevents Schiff base formation with the cofactor, inactive mutant Arabidopsis thaliana
2.6.1.78 R445G site-directed mutagenesis, inactive mutant Arabidopsis thaliana
2.6.1.78 T84V site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.78 T84V/K169V site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.79 A168G site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.79 E108K site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.79 K169S site-directed mutagenesis, inactive with aspartate and glutamate Arabidopsis thaliana
2.6.1.79 K169V site-directed mutagenesis, inactive with glutamate, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.79 K306A site-directed mutagenesis, structure comparison with wild-type, overview. The alanine substitution of Lys306 prevents Schiff base formation with the cofactor, inactive mutant Arabidopsis thaliana
2.6.1.79 R445G site-directed mutagenesis, inactive mutant Arabidopsis thaliana
2.6.1.79 T84V site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana
2.6.1.79 T84V/K169V site-directed mutagenesis, altered substrate binding kinetics compared to wild-type Arabidopsis thaliana

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.6.1.1 cysteine dokcing sturdy with wild-type and mutant enzymes Arabidopsis thaliana
2.6.1.78 cysteine docking study with wild-type and mutant enzymes Arabidopsis thaliana
2.6.1.79 cysteine dokcing sturdy with wild-type and mutant enzymes Arabidopsis thaliana

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.6.1.1 additional information
-
 additional information steady-state kinetics analysis Arabidopsis thaliana
2.6.1.1 0.46
-
 2-oxoglutarate pH 7.5, 25°C, recombinant mutant T84V Arabidopsis thaliana
2.6.1.1 1
-
 2-oxoglutarate pH 7.5, 25°C, recombinant mutant E108K Arabidopsis thaliana
2.6.1.1 1.1
-
 2-oxoglutarate pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana
2.6.1.1 1.2
-
 2-oxoglutarate pH 7.5, 25°C, recombinant mutant A168G Arabidopsis thaliana
2.6.1.1 1.6
-
 L-aspartate pH 7.5, 25°C, recombinant mutant T84V Arabidopsis thaliana
2.6.1.1 1.9
-
 L-aspartate pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana
2.6.1.1 2.8
-
 L-aspartate pH 7.5, 25°C, recombinant mutant E108K Arabidopsis thaliana
2.6.1.1 3.8
-
 L-aspartate pH 7.5, 25°C, recombinant mutant A168G Arabidopsis thaliana
2.6.1.78 additional information
-
 additional information steady-state kinetics analysis Arabidopsis thaliana
2.6.1.78 0.17
-
 prephenate pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana
2.6.1.78 0.48
-
 prephenate pH 7.5, 25°C, recombinant mutant A168G Arabidopsis thaliana
2.6.1.78 0.55
-
 prephenate pH 7.5, 25°C, recombinant mutant T84V Arabidopsis thaliana
2.6.1.78 2
-
 prephenate pH 7.5, 25°C, recombinant mutant E108K Arabidopsis thaliana
2.6.1.79 additional information
-
 additional information steady-state kinetics analysis Arabidopsis thaliana

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.6.1.1 L-aspartate + 2-oxoglutarate Arabidopsis thaliana
-
 oxaloacetate + L-glutamate
-
 r
2.6.1.78 L-arogenate + oxaloacetate Arabidopsis thaliana
-
 L-aspartate + prephenate
-
 r
2.6.1.79 L-arogenate + 2-oxoglutarate Arabidopsis thaliana
-
 L-glutamate + prephenate
-
 r

Organism

EC Number Organism UniProt Comment Textmining
2.6.1.1 Arabidopsis thaliana Q9SIE1
-
-
2.6.1.78 Arabidopsis thaliana Q9SIE1
-
-
2.6.1.79 Arabidopsis thaliana Q9SIE1
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
2.6.1.1 L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate catalytic reaction mechanism, overview Arabidopsis thaliana
a
2.6.1.78 L-arogenate + oxaloacetate = prephenate + L-aspartate catalytic reaction mechanism, overview Arabidopsis thaliana
a
2.6.1.79 L-arogenate + 2-oxoglutarate = prephenate + L-glutamate catalytic reaction mechanism, overview Arabidopsis thaliana
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.6.1.1 L-aspartate + 2-oxoglutarate
-
 Arabidopsis thaliana oxaloacetate + L-glutamate
-
 r
2.6.1.78 L-arogenate + oxaloacetate
-
 Arabidopsis thaliana L-aspartate + prephenate
-
 r
2.6.1.78 L-aspartate + prephenate
-
 Arabidopsis thaliana L-arogenate + oxaloacetate
-
 r
2.6.1.79 L-arogenate + 2-oxoglutarate
-
 Arabidopsis thaliana L-glutamate + prephenate
-
 r
2.6.1.79 L-glutamate + prephenate
-
 Arabidopsis thaliana L-arogenate + 2-oxoglutarate
-
 r

Subunits

EC Number Subunits Comment Organism
2.6.1.1 homodimer AtPAT crystallizes as a homodimer. Each monomer of AtPAT consists of 15 alpha-helices and 9 beta-strands divided between two structural domains. The N-terminal domain (Lys115-Leu353) contains two sets of three alpha-helices surrounding six parallel and one anti-parallel beta-strand. Two additional alpha-helices in the PLP-binding pocket, as well as the alpha-helix connecting the N- and C-terminal domains, complete the N-terminal domain. The smaller C-terminal domain contains part of the N-terminal region (Ser71-Pro114) and residues Gly354 through Leu469, totaling five alpha-helices and two beta-strands. The N-terminal flexible loop (Ser71-Ser82) and features of the N-terminal domain form the dimer interface Arabidopsis thaliana
2.6.1.78 homodimer AtPAT crystallizes as a homodimer. Each monomer of AtPAT consists of 15 alpha-helices and 9 beta-strands divided between two structural domains. The N-terminal domain (Lys115-Leu353) contains two sets of three a-helices surrounding six parallel and one anti-parallel beta-strand. Two additional alpha-helices in the PLP-binding pocket, as well as the a-helix connecting the N- and C-terminal domains, complete the N-terminal domain. The smaller C-terminal domain contains part of the N-terminal region (Ser71-Pro114) and residues Gly354 through Leu469, totaling five alpha-helices and two beta-strands. The N-terminal flexible loop (Ser71-Ser82) and features of the N-terminal domain form the dimer interface Arabidopsis thaliana
2.6.1.79 homodimer AtPAT crystallizes as a homodimer. Each monomer of AtPAT consists of 15 alpha-helices and 9 beta-strands divided between two structural domains. The N-terminal domain (Lys115-Leu353) contains two sets of three a-helices surrounding six parallel and one anti-parallel beta-strand. Two additional alpha-helices in the PLP-binding pocket, as well as the a-helix connecting the N- and C-terminal domains, complete the N-terminal domain. The smaller C-terminal domain contains part of the N-terminal region (Ser71-Pro114) and residues Gly354 through Leu469, totaling five alpha-helices and two beta-strands. The N-terminal flexible loop (Ser71-Ser82) and features of the N-terminal domain form the dimer interface Arabidopsis thaliana

Synonyms

EC Number Synonyms Comment Organism
2.6.1.1 AtPAT
-
 Arabidopsis thaliana
2.6.1.1 bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase UniProt Arabidopsis thaliana
2.6.1.1 class Ibeta AAT
-
 Arabidopsis thaliana
2.6.1.1 More cf. EC 2.6.1.78 and EC 2.6.1.79 Arabidopsis thaliana
2.6.1.1 Pat
-
 Arabidopsis thaliana
2.6.1.1 prephenate aminotransferase
-
 Arabidopsis thaliana
2.6.1.78 AtPAT
-
 Arabidopsis thaliana
2.6.1.78 bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase UniProt Arabidopsis thaliana
2.6.1.78 class Ibeta AAT
-
 Arabidopsis thaliana
2.6.1.78 More cf. EC 2.6.1.79 and EC 2.6.1.1 Arabidopsis thaliana
2.6.1.78 Pat
-
 Arabidopsis thaliana
2.6.1.78 prephenate aminotransferase
-
 Arabidopsis thaliana
2.6.1.79 AtPAT
-
 Arabidopsis thaliana
2.6.1.79 bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase UniProt Arabidopsis thaliana
2.6.1.79 class Ibeta AAT
-
 Arabidopsis thaliana
2.6.1.79 More cf. EC 2.6.1.78 and EC 2.6.1.1 Arabidopsis thaliana
2.6.1.79 Pat
-
 Arabidopsis thaliana
2.6.1.79 prephenate aminotransferase
-
 Arabidopsis thaliana

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.6.1.1 25
-
 assay at Arabidopsis thaliana
2.6.1.78 25
-
 assay at Arabidopsis thaliana
2.6.1.79 25
-
 assay at Arabidopsis thaliana

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.6.1.1 1.83
-
 2-oxoglutarate pH 7.5, 25°C, recombinant mutant T84V Arabidopsis thaliana
2.6.1.1 1.83
-
 L-aspartate pH 7.5, 25°C, recombinant mutant T84V Arabidopsis thaliana
2.6.1.1 4.83
-
 L-aspartate pH 7.5, 25°C, recombinant mutant A168G Arabidopsis thaliana
2.6.1.1 7.83
-
 2-oxoglutarate pH 7.5, 25°C, recombinant mutant A168G Arabidopsis thaliana
2.6.1.1 8.33
-
 2-oxoglutarate pH 7.5, 25°C, recombinant mutant E108K Arabidopsis thaliana
2.6.1.1 8.33
-
 L-aspartate pH 7.5, 25°C, recombinant mutant E108K Arabidopsis thaliana
2.6.1.1 9.33
-
 L-aspartate pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana
2.6.1.1 10.16
-
 2-oxoglutarate pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana
2.6.1.78 1.18
-
 prephenate pH 7.5, 25°C, recombinant mutant T84V Arabidopsis thaliana
2.6.1.78 2.67
-
 prephenate pH 7.5, 25°C, recombinant mutant E108K Arabidopsis thaliana
2.6.1.78 3.83
-
 prephenate pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana
2.6.1.78 6.67
-
 prephenate pH 7.5, 25°C, recombinant mutant A168G Arabidopsis thaliana

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.6.1.1 7.5
-
 assay at Arabidopsis thaliana
2.6.1.78 7.5
-
 assay at Arabidopsis thaliana
2.6.1.79 7.5
-
 assay at Arabidopsis thaliana

Cofactor

EC Number Cofactor Comment Organism Structure
2.6.1.1 pyridoxal 5'-phosphate PLP, dependent on, PLP is bound in the active site of each chain in the wild-type structure. In the AtPAT crystal structure, PLP is covalently linked to the epsilon-nitrogen of Lys306 to form the internal aldimine (i.e. Schiff base). Trp193 and Ile274 position the ring of PLP through pi-pi stacking and van der Waals interactions, respectively. The pyridine ring nitrogen of PLP forms a charge-charge interaction with the side chain of Asp272 Arabidopsis thaliana
2.6.1.78 pyridoxal 5'-phosphate PLP, dependent on, PLP is bound in the active site of each chain in the wild-type structure. In the AtPAT crystal structure, PLP is covalently linked to the epsilon-nitrogen of Lys306 to form the internal aldimine (i.e. Schiff base). Trp193 and Ile274 position the ring of PLP through pi-pi stacking and van der Waals interactions, respectively. The pyridine ring nitrogen of PLP forms a charge-charge interaction with the side chain of Asp272 Arabidopsis thaliana
2.6.1.79 pyridoxal 5'-phosphate PLP, dependent on, PLP is bound in the active site of each chain in the wild-type structure. In the AtPAT crystal structure, PLP is covalently linked to the epsilon-nitrogen of Lys306 to form the internal aldimine (i.e. Schiff base). Trp193 and Ile274 position the ring of PLP through pi-pi stacking and van der Waals interactions, respectively. The pyridine ring nitrogen of PLP forms a charge-charge interaction with the side chain of Asp272 Arabidopsis thaliana

IC50 Value

EC Number IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
2.6.1.78 0.56
-
 versus 2-oxoglutarate, pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana cysteine
2.6.1.78 0.75
-
 versus prephenate, pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana cysteine
2.6.1.79 0.56
-
 versus 2-oxoglutarate, pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana cysteine
2.6.1.79 0.75
-
 versus prephenate, pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana cysteine

General Information

EC Number General Information Comment Organism
2.6.1.1 additional information key residues, such as Glu108, are involved in both keto acid and amino acid substrate specificities and probably contribute to the evolution of PAT activity among class Ibeta AAT enzymes, ligand binding study, molecular mechanisms underlying recognition of keto acid and amino acid substrates, overview. Lys306 is the catalytic Lys in AtPAT Arabidopsis thaliana
2.6.1.78 additional information key residues, such as Glu108, are involved in both keto acid and amino acid substrate specificities and probably contribute to the evolution of PAT activity among class Ibeta AAT enzymes, ligand binding study, molecular mechanisms underlying recognition of keto acid and amino acid substrates, overview. Lys306 is the catalytic Lys in AtPAT Arabidopsis thaliana
2.6.1.79 additional information key residues, such as Glu108, are involved in both keto acid and amino acid substrate specificities and probably contribute to the evolution of PAT activity among class Ibeta AAT enzymes, ligand binding study, molecular mechanisms underlying recognition of keto acid and amino acid substrates, overview. Lys306 is the catalytic Lys in AtPAT Arabidopsis thaliana

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
2.6.1.1 1.14
-
 L-aspartate pH 7.5, 25°C, recombinant mutant T84V Arabidopsis thaliana
2.6.1.1 1.27
-
 L-aspartate pH 7.5, 25°C, recombinant mutant A168G Arabidopsis thaliana
2.6.1.1 2.98
-
 L-aspartate pH 7.5, 25°C, recombinant mutant E108K Arabidopsis thaliana
2.6.1.1 3.98
-
 2-oxoglutarate pH 7.5, 25°C, recombinant mutant T84V Arabidopsis thaliana
2.6.1.1 4.91
-
 L-aspartate pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana
2.6.1.1 6.53
-
 2-oxoglutarate pH 7.5, 25°C, recombinant mutant A168G Arabidopsis thaliana
2.6.1.1 8.33
-
 2-oxoglutarate pH 7.5, 25°C, recombinant mutant E108K Arabidopsis thaliana
2.6.1.1 9.24
-
 2-oxoglutarate pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana
2.6.1.78 1.34
-
 prephenate pH 7.5, 25°C, recombinant mutant E108K Arabidopsis thaliana
2.6.1.78 2.15
-
 prephenate pH 7.5, 25°C, recombinant mutant T84V Arabidopsis thaliana
2.6.1.78 13.9
-
 prephenate pH 7.5, 25°C, recombinant mutant A168G Arabidopsis thaliana
2.6.1.78 22.53
-
 prephenate pH 7.5, 25°C, recombinant wild-type enzyme Arabidopsis thaliana