Cloned (Comment) | Organism |
---|---|
gene Dret_1107, construction of the synthetic gene coding the transaminase Dret from Desulfohalobium retbaense, recombinant expression | Desulfohalobium retbaense |
Protein Variants | Comment | Organism |
---|---|---|
additional information | construction of a synthetic gene coding the transaminase Dret from Desulfohalobium retbaense. The following structures are chosen as the templates for constructing the Dret model: (a) (R)-TA from Nectria haematococca (PDB ID 4CMD) residues 7-44 for the modeling of the N-terminus of Dret (identity of 22%), (b) DAAT from Bacillus sp. YM-1 (bsDAAT, PDB ID 3DAA) residues 45-302 (identity of 26%), (c) BCAT from Geoglobus acetivorans (PDB ID 5E25) residues 302-314 (identity of 28%). The amino acid sequences required for modeling by homology are fitted. Comparing the structure of Dret with the structure of the canonical bsDAAT (PDB ID 3DAA) shows a series of differences in the structure of the active sites | Desulfohalobium retbaense |
Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
---|---|---|---|
70000 | - |
recombinant enzyme, gel fitration | Desulfohalobium retbaense |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
D-leucine + 2-oxoglutarate | Desulfohalobium retbaense | - |
4-methyl-2-oxopentanoate + D-glutamate | - |
r | |
D-leucine + 2-oxoglutarate | Desulfohalobium retbaense ATCC 49708 | - |
4-methyl-2-oxopentanoate + D-glutamate | - |
r | |
D-leucine + 2-oxoglutarate | Desulfohalobium retbaense JCM 16813 | - |
4-methyl-2-oxopentanoate + D-glutamate | - |
r | |
D-leucine + 2-oxoglutarate | Desulfohalobium retbaense DSM 5692 | - |
4-methyl-2-oxopentanoate + D-glutamate | - |
r | |
D-leucine + 2-oxoglutarate | Desulfohalobium retbaense HR100 | - |
4-methyl-2-oxopentanoate + D-glutamate | - |
r |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Desulfohalobium retbaense | C8X272 | - |
- |
Desulfohalobium retbaense ATCC 49708 | C8X272 | - |
- |
Desulfohalobium retbaense DSM 5692 | C8X272 | - |
- |
Desulfohalobium retbaense HR100 | C8X272 | - |
- |
Desulfohalobium retbaense JCM 16813 | C8X272 | - |
- |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
D-leucine + 2-oxoglutarate | - |
Desulfohalobium retbaense | 4-methyl-2-oxopentanoate + D-glutamate | - |
r | |
D-leucine + 2-oxoglutarate | - |
Desulfohalobium retbaense ATCC 49708 | 4-methyl-2-oxopentanoate + D-glutamate | - |
r | |
D-leucine + 2-oxoglutarate | - |
Desulfohalobium retbaense JCM 16813 | 4-methyl-2-oxopentanoate + D-glutamate | - |
r | |
D-leucine + 2-oxoglutarate | - |
Desulfohalobium retbaense DSM 5692 | 4-methyl-2-oxopentanoate + D-glutamate | - |
r | |
D-leucine + 2-oxoglutarate | - |
Desulfohalobium retbaense HR100 | 4-methyl-2-oxopentanoate + D-glutamate | - |
r | |
additional information | comparison of the active sites of Dret with D- and L-leucine in presence of PLP, overview. The absence of the Arg98* residue, that is conservative for the DAATs in the active site of Dret, is presumably compensated by the Arg54* residue, the functional group occupies the same spatial position as the Arg98* functional group in the bsDAAT. This residue forms two stable hydrogen bonds with D-leucine in the enzyme-substrate complex. In the case of L-leucine, only one of the two bonds is preserved, and a new hydrogen bond is formed between the alpha-COO- group of L-leucine and His53*. This leads to the disruption of the structure of the active site and explains the absence of a reaction with L-leucine. The binding of D-leucine by the residues of the active site of Dret promotes efficient transformations of the substrate by the mechanism determined for transaminases | Desulfohalobium retbaense | ? | - |
- |
|
additional information | comparison of the active sites of Dret with D- and L-leucine in presence of PLP, overview. The absence of the Arg98* residue, that is conservative for the DAATs in the active site of Dret, is presumably compensated by the Arg54* residue, the functional group occupies the same spatial position as the Arg98* functional group in the bsDAAT. This residue forms two stable hydrogen bonds with D-leucine in the enzyme-substrate complex. In the case of L-leucine, only one of the two bonds is preserved, and a new hydrogen bond is formed between the alpha-COO- group of L-leucine and His53*. This leads to the disruption of the structure of the active site and explains the absence of a reaction with L-leucine. The binding of D-leucine by the residues of the active site of Dret promotes efficient transformations of the substrate by the mechanism determined for transaminases | Desulfohalobium retbaense ATCC 49708 | ? | - |
- |
|
additional information | comparison of the active sites of Dret with D- and L-leucine in presence of PLP, overview. The absence of the Arg98* residue, that is conservative for the DAATs in the active site of Dret, is presumably compensated by the Arg54* residue, the functional group occupies the same spatial position as the Arg98* functional group in the bsDAAT. This residue forms two stable hydrogen bonds with D-leucine in the enzyme-substrate complex. In the case of L-leucine, only one of the two bonds is preserved, and a new hydrogen bond is formed between the alpha-COO- group of L-leucine and His53*. This leads to the disruption of the structure of the active site and explains the absence of a reaction with L-leucine. The binding of D-leucine by the residues of the active site of Dret promotes efficient transformations of the substrate by the mechanism determined for transaminases | Desulfohalobium retbaense JCM 16813 | ? | - |
- |
|
additional information | comparison of the active sites of Dret with D- and L-leucine in presence of PLP, overview. The absence of the Arg98* residue, that is conservative for the DAATs in the active site of Dret, is presumably compensated by the Arg54* residue, the functional group occupies the same spatial position as the Arg98* functional group in the bsDAAT. This residue forms two stable hydrogen bonds with D-leucine in the enzyme-substrate complex. In the case of L-leucine, only one of the two bonds is preserved, and a new hydrogen bond is formed between the alpha-COO- group of L-leucine and His53*. This leads to the disruption of the structure of the active site and explains the absence of a reaction with L-leucine. The binding of D-leucine by the residues of the active site of Dret promotes efficient transformations of the substrate by the mechanism determined for transaminases | Desulfohalobium retbaense DSM 5692 | ? | - |
- |
|
additional information | comparison of the active sites of Dret with D- and L-leucine in presence of PLP, overview. The absence of the Arg98* residue, that is conservative for the DAATs in the active site of Dret, is presumably compensated by the Arg54* residue, the functional group occupies the same spatial position as the Arg98* functional group in the bsDAAT. This residue forms two stable hydrogen bonds with D-leucine in the enzyme-substrate complex. In the case of L-leucine, only one of the two bonds is preserved, and a new hydrogen bond is formed between the alpha-COO- group of L-leucine and His53*. This leads to the disruption of the structure of the active site and explains the absence of a reaction with L-leucine. The binding of D-leucine by the residues of the active site of Dret promotes efficient transformations of the substrate by the mechanism determined for transaminases | Desulfohalobium retbaense HR100 | ? | - |
- |
Synonyms | Comment | Organism |
---|---|---|
DAAT | - |
Desulfohalobium retbaense |
Dret | - |
Desulfohalobium retbaense |
Dret_1107 | - |
Desulfohalobium retbaense |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
pyridoxal 5'-phosphate | PLP | Desulfohalobium retbaense |
General Information | Comment | Organism |
---|---|---|
evolution | transaminases with the fold type IV of the PLP binding domain vary in substrate specificity and include enzymes specific to both D- and L-amino acids. D-amino acid transaminases (DAATs), branched-chain L-amino acid transaminases (BCATs), and (R)-primary amine specific transaminases ((R)-TA) are distinguished among the enzymes with the fold type IV | Desulfohalobium retbaense |
additional information | molecular mechanism of stereospecificity toward D-leucine of the transaminase from Desulfohalobium retbaense, molecular dynamic simulations, overview. HOmology modeling using the structure of the canonical bsDAAT (PDB ID 3DAA) revealing a series of differences in the structure of the active sites | Desulfohalobium retbaense |