Overview for MACiE Entry M0110
EC Number: 18.104.22.168 (A member of the Oxidoreductases, Acting on the CH-NH2 group of donors, With oxygen as acceptor)
Enzyme Name: D-amino-acid oxidase
Biological Species: Rhodotorula gracilis (Yeast)
Catalytic Chain UniprotKB Accession Codes:
Representative PDB Code: 1c0p - D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLYOCCUPIED BIATOMIC SPECIES (Resolution = 1.20 Å).
Catalytic CATH Codes:
"Other" CATH Codes:
- 22.214.171.124 - D-Amino Acid Oxidase, subunit A, domain 2
Display structure information
It is unknown whether this reaction is reversible or not.
Overall Comment: There are two main competing alternative mechanisms for this reaction. The carbanion mechanism in which the alpha hydrogen of the amino acid is abstracted as a proton, requiring an active site base, which was suggested upon the observation that pig kidney DAAO catalyses the elimination of halide from beta-halogenated amino acids. The other mechanism is the hydride mechanism, in which the alpha hydrogen is transferred (as a hydride) to the N5 of the flavin. The second mechanism is shown here and is supported by high resolution crystal structures, kinetic isotope effects and free energy correlation calculations .
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Stepwise Description of the Reaction
|Step 1||Water deprotonates Ser1335, which deprotonates the amine of the D-amino acid, eliminating a hydride ion, which adds to FAD.|
|Step 2||The FAD undergoes double bond rearrangement which causes a single electron to be transferred to a dioxygen molecule.|
|Step 3||The dioxygen molecule undergoes a homolytic reaction in which it colligates to FAD, with concomitant deprotonation of water.|
|Step 4||The peroxo group deprotonates FAD, which initiates the elimination of hydrogen peroxide.|
|Step 5||The product of the enzyme undergoes spontaneous hydrolysis outside of the active site to produce ammonium and the 2-oxo acid.|
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Catalytic Residues Involved
||Location of Function
||Main Chain Carbonyl
||Main Chain Amide
Main Chain Carbonyl
||Main Chain Carbonyl
Organic Cofactors for M0110
- S. Umhau et al. (2000), Proc. Natl Acad. Sci. USA, 97, 12463-12468. The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.
- A. Boselli et al. (2004), Biochim. Biophys. Acta, 1702, 19-32. On the mechanism of Rhodotorula gracilis D-amino acid oxidase: role of the active site serine 335.
- M. S. Pilone (2000), Cell. Mol. Life Sci., 57, 1732-1747. D-Amino acid oxidase: new findings.
Homologue information for M0110 (1c0p)
MACiE Homologues (within the PDB)
MACiE Homologues (within UniprotKB/SwissProt)
Entries with at least one Catalytic CATH code in common (different mechanisms):
|M0255 ||alcohol dehydrogenase |
|M0092 ||UDP-glucose 6-dehydrogenase |
|M0021 ||malate dehydrogenase (oxaloacetate-decarboxylating) |
|M0227 ||GDP-L-fucose synthase |
|M0237 ||pteridine reductase |
|M0116 ||NAD(P)+ transhydrogenase (AB-specific) |
|M0142 ||ferredoxin-NADP+ reductase |
|M0090 ||adenosylhomocysteinase |
|M0226 ||UDP-sulfoquinovose synthase |
|M0228 ||dTDP-glucose 4,6-dehydratase |
|M0188 ||UDP-glucose 4-epimerase |
View a comparison of the other reactions in MACiE with the CATH domain 126.96.36.1990
Links to this entry in other databases