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Literature summary for 5.4.3.10 extracted from
- Ironing out their differences Dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase (2015), ACS Chem. Biol., 10, 989-997 .
No PubMed abstract available
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| crystal structure analysis of TcdPAM, PDB ID 3NZ4 | Taxus canadensis |
| crystal structure analysis of TcPAM mutants, PDB IDs 4V2R and 4V2Q | Taxus chinensis |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| A77T/I79S/C89T/L97G | site-directed mutagenesis, the mutant shows an altered structure compared to wild-type enzyme with reduced beta-ladder and 3_10-helix contents | Taxus chinensis |
| L97G | site-directed mutagenesis, the mutant shows an altered structure compared to wild-type enzyme, the mutant has a significant increase in 310-helix and beta-ladder, compared to wild-type, with the highest coil percent among the PAM variants and improved activity. The mutant shows reduced temperature stability and optimum for PAM activity, in contrast to PAL activity | Taxus chinensis |
| L97G/A77T/C89T | site-directed mutagenesis, the mutant shows an altered structure compared to wild-type enzyme with reduced beta-ladder and 3_10-helix contents | Taxus chinensis |
| L97G/C89T | site-directed mutagenesis, the mutant shows an altered structure compared to wild-type enzyme, the mutant has a significant increase in 310-helix and beta-ladder compared to wild-type. The mutant shows reduced temperature stability and optimum for PAM activity, in contrast to PAL activity | Taxus chinensis |
| additional information | mutation of the inner loop region, that closes the active site of PAM, within PAM (PAM residues 77-97) in a stepwise approach. Almost all of the single loop mutations trigger a lyase phenotype in PAM. Experimental and computational evidence suggest that the induced lyase features result from inner loop mobility enhancements, which are possibly caused by a 310-helix cluster, flanking alpha-helices, and hydrophobic interactions. The application of wild-type PAM for the synthesis of beta-amino acids is hindered by low reaction rates and the mixture of alpha-Phe and beta-Phe generated from the asymmetric synthetic route. Molecular dynamic simulations | Taxus chinensis |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.008 | - |
D-alpha-phenylalanine | pH and temperature not specified in the publication, recombinant wild-type enzyme | Taxus chinensis |  |
| 0.028 | - |
L-beta-phenylalanine | pH and temperature not specified in the publication, recombinant wild-type enzyme | Taxus chinensis | |
| 0.058 | - |
D-alpha-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G/C89T | Taxus chinensis | |
| 0.067 | - |
D-alpha-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G | Taxus chinensis | |
| 0.29 | - |
L-beta-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G/C89T | Taxus chinensis | |
| 0.31 | - |
L-beta-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G | Taxus chinensis | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-alpha-phenylalanine | Taxus chinensis | - |
L-beta-phenylalanine | - |
r | |
| L-phenylalanine | Taxus canadensis | - |
L-beta-phenylalanine | - |
r | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Taxus canadensis | Q6GZ04 | - |
- |
| Taxus chinensis | Q68G84 | i.e. Taxus chinensis | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-alpha-phenylalanine | - |
Taxus chinensis | L-beta-phenylalanine | - |
r | |
| L-beta-phenylalanine | - |
Taxus chinensis | D-alpha-phenylalanine | - |
r | |
| L-phenylalanine | - |
Taxus canadensis | L-beta-phenylalanine | - |
r | |
| L-phenylalanine | L-alpha-phenylalanine | Taxus canadensis | L-beta-phenylalanine | - |
r | |
| additional information | the enzyme catalyzes a 2,3-amine shift that reversibly interconverts alpha-Phe to beta-Phe | Taxus canadensis | ? | - |
? | |
| additional information | the enzyme catalyzes a 2,3-amine shift that reversibly interconverts alpha-Phe to beta-Phe | Taxus chinensis | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| More | secondary structural analysis of the simulated PAM systems at the resting state, wild-type and mutant enzymes, overview | Taxus chinensis |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| PAM | - |
Taxus canadensis |
| PAM | - |
Taxus chinensis |
| phenylalanine AM | - |
Taxus canadensis |
| phenylalanine AM | - |
Taxus chinensis |
| phenylalanine aminomutase | - |
Taxus canadensis |
| phenylalanine aminomutase | - |
Taxus chinensis |
| TcPAM | - |
Taxus canadensis |
| TcPAM | - |
Taxus chinensis |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 70 | - |
- |
Taxus chinensis |
Temperature Range [°C]
| Temperature Minimum [°C] | Temperature Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 30 | 70 | no activity at 15°C, increasing activity with increasing temperature, highest at 70°C, profile overview | Taxus chinensis |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.0032 | - |
D-alpha-phenylalanine | pH and temperature not specified in the publication, recombinant wild-type enzyme | Taxus chinensis | |
| 0.0088 | - |
D-alpha-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G/C89T | Taxus chinensis | |
| 0.0092 | - |
L-beta-phenylalanine | pH and temperature not specified in the publication, recombinant wild-type enzyme | Taxus chinensis | |
| 0.0184 | - |
D-alpha-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G | Taxus chinensis | |
| 0.062 | - |
L-beta-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G/C89T | Taxus chinensis | |
| 0.117 | - |
L-beta-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G | Taxus chinensis | |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| 3,5-dihydro-5-methylidene-4H-imidazol-4-one | i.e. MIO, essential cofactor | Taxus canadensis | |
| 3,5-dihydro-5-methylidene-4H-imidazol-4-one | i.e. MIO, essential cofactor | Taxus chinensis | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | structural determinant that dictates the activity differences between a phenylalanine ammonia lyase (PAL, EC 4.3.1.24) and aminomutase (PAM), overview. An inner loop region closes the active sites of both PAM and PAL. The inner loop is a structural determinant of the lyase and mutase activities of PAM. Three-dimensional structure comparisons of Taxus canadensis PAM with PAM from Taxus chinensis and phenylalanine ammonia lyase from Petroselinum crispum (PcPAL) | Taxus canadensis |
| evolution | structural determinant that dictates the activity differences between a phenylalanine ammonia lyase (PAL, EC 4.3.1.24) and aminomutase (PAM), overview. An inner loop region closes the active sites of both PAM and PAL. The inner loop is a structural determinant of the lyase and mutase activities of PAM. Three-dimensional structure comparisons of Taxus chinensis PAM with PAM from Taxus canadensis and phenylalanine ammonia lyase from Petroselinum crispum (PcPAL) | Taxus chinensis |
| additional information | the inner loop is a structural determinant of the lyase and mutase activities of PAM | Taxus canadensis |
| additional information | the inner loop is a structural determinant of the lyase and mutase activities of PAM. Three-dimensional structure comparisons of Taxus chinensis PAM with PAM from Taxus canadensis and phenylalanine ammonia lyase from Petroselinum crispum (PcPAL). The latter contains an open inner loop conformation. The active-site inner loop, which contains the catalytic base Tyr, appears more rigid in PAM and more open or flexible in PAL. The rigidity of this loop in PAM is considered crucial for sequestering the trans-cinnamic acid and MIO-amine adduct in the active site to promote readdition of the amino-group to either the alpha- or beta-carbon positions of trans-cinnamic acid. Molecular dynamic simulations | Taxus chinensis |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.15 | - |
D-alpha-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G/C89T | Taxus chinensis | |
| 0.21 | - |
L-beta-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G/C89T | Taxus chinensis | |
| 0.28 | - |
D-alpha-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G | Taxus chinensis | |
| 0.32 | - |
L-beta-phenylalanine | pH and temperature not specified in the publication, recombinant wild-type enzyme | Taxus chinensis | |
| 0.38 | - |
L-beta-phenylalanine | pH and temperature not specified in the publication, recombinant mutant L97G | Taxus chinensis | |
| 0.4 | - |
D-alpha-phenylalanine | pH and temperature not specified in the publication, recombinant wild-type enzyme | Taxus chinensis | |
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