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

BRENDA support

Literature summary for 2.6.1.21 extracted from

  • Khrenova, M.; Zavyalova, S.; Bezsudnova, E.
    Molecular mechanism of stereospecificity toward D-leucine of the transaminase from Desulfohalobium retbaense revealed by molecular dynamic simulations (2020), Moscow Univ. Chem. Bull., 75, 167-171 .
No PubMed abstract available

Cloned(Commentary)

Cloned (Comment) Organism
gene Dret_1107, construction of the synthetic gene coding the transaminase Dret from Desulfohalobium retbaense, recombinant expression Desulfohalobium retbaense

Protein Variants

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 [Da] Molecular Weight Maximum [Da] Comment Organism
70000
-
recombinant enzyme, gel fitration Desulfohalobium retbaense

Natural Substrates/ Products (Substrates)

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

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 and Products (Substrate)

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

Synonyms Comment Organism
DAAT
-
Desulfohalobium retbaense
Dret
-
Desulfohalobium retbaense
Dret_1107
-
Desulfohalobium retbaense

Cofactor

Cofactor Comment Organism Structure
pyridoxal 5'-phosphate PLP Desulfohalobium retbaense

General Information

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