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Catalytic Site Atlas

CSA LITERATURE entry for 1daa

E.C. nameD-amino-acid transaminase
SpeciesBacillus sp. (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1daaThere are 12 Homologs
CSA Entries With UniProtID P19938
CSA Entries With EC Number
PDBe Entry 1daa
PDBSum Entry 1daa
MACiE Entry M0066

Literature Report

IntroductionD-Amino acid aminotransferase (D-aAt) catalyses the transamination of various D-amino acids, forming their respective keto acids. The enzyme has no sequence similarity to the well studied L-amino acid aminotransferase but does have significant sequence overlap with a bacterial branched-chain L-amino acid aminotransferase and 4-amino-4-deoxychorismate lyase. D-aAt is essential for the synthesis of bacterial cell wall components and has been a target of research in the development of antimicrobial agents.
MechansimUpon binding of a substrate amino acid, a transaldimation reaction occurs, releasing Lys145 from the internal aldimine and forming an external aldimine between the substrate and PLP cofactor. Lys145 then acts as the general base in the next step, driving the 1,3 prototropic shift that converts the internal aldimine into a ketimine intermediate. Next, this ketimine is hydrolysed to form pyridoxamine phosphate and an alpha-keto acid. The second half of the reaction is the reversal of these steps with a different keto acid.

Catalytic Sites for 1daa

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA145146macie:sideChainThe residue forms a covalent Schiff base link to the PLP cofactor. Once the residue has been displaced during the formation of the external aldimine, the basic side group is free to act as a general base, driving the 1,3 prototropic shift. This converts the internal aldimine to the ketimine intermediate.
GluA177178macie:sideChainThe residue's negatively charged side chain hydrogen bonds to the nitrogen of the pyridinium ring , an interaction which is thought to stabilise the carbanion intermediates of the reaction.
TyrA3132macie:sideChainThe residue's phenolic oxygen hydrogen bonds to the catalytic base Lys145. This interaction is thought to activate Lys145 towards its function as a general base. Mutagenesis has also implicated the residue in maintaining stereochemical fidelity.

Literature References

Sugio S
Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity.
Biochemistry 1995 34 9661-9669
PubMed: 7626635
Peisach D
Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.
Biochemistry 1998 37 4958-4967
PubMed: 9538014
van Ophem PW
Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity.
Biochemistry 1999 38 1323-1331
PubMed: 9930994