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Overview for MACiE Entry M0110

Version history

General Information

EC Number: 1.4.3.3 (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:

  • 3.30.9.10 - D-Amino Acid Oxidase, subunit A, domain 2

Display structure information

Overall Reaction:

Image of D-amino acid

Image of oxygen

Image of water

right arrow

Image of ammonium

Image of 2-oxo acid

Image of hydrogen peroxide

D-amino acid
C00405
CHEBI:59871
oxygen
C00007
CHEBI:15379
water
C00001
CHEBI:15377
ammonium
C01342
CHEBI:28938
2-oxo acid
C00161
CHEBI:35179
hydrogen peroxide
C00027
CHEBI:16240

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 [1].


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Stepwise Description of the Reaction

Step 1Water deprotonates Ser1335, which deprotonates the amine of the D-amino acid, eliminating a hydride ion, which adds to FAD.
Step 2The FAD undergoes double bond rearrangement which causes a single electron to be transferred to a dioxygen molecule.
Step 3The dioxygen molecule undergoes a homolytic reaction in which it colligates to FAD, with concomitant deprotonation of water.
Step 4The peroxo group deprotonates FAD, which initiates the elimination of hydrogen peroxide.
Step 5The 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

Type Number Chain Location of Function
Ser 1335 A Main Chain Carbonyl
Side Chain
Asn 1054 A Main Chain Amide
Main Chain Carbonyl
Gln 1339 A Main Chain Carbonyl

Organic Cofactors for M0110

Type Identity Chain
FAD FAD 1363 Overview

References

  1. 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.
    Medline: 11070076
  2. 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.
    Medline: 15450847
  3. M. S. Pilone (2000), Cell. Mol. Life Sci., 57, 1732-1747. D-Amino acid oxidase: new findings.
    Medline: 11130179

Homologue information for M0110 (1c0p)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0255 alcohol dehydrogenase
1.1.1.1
1mg5 3.40.50.720
0.42370.18Compare
M0092 UDP-glucose 6-dehydrogenase
1.1.1.22
1dli 3.40.50.720
0.5250.1349Compare
M0021 malate dehydrogenase (oxaloacetate-decarboxylating)
1.1.1.38
1do8 3.40.50.720
0.50.1407Compare
M0227 GDP-L-fucose synthase
1.1.1.271
1e6u 3.40.50.720
0.48830.1999Compare
M0237 pteridine reductase
1.5.1.33
2c7v 3.40.50.720
0.62660Compare
M0116 NAD(P)+ transhydrogenase (AB-specific)
1.6.1.2
1hzz 3.40.50.720
0.23330Compare
M0142 ferredoxin-NADP+ reductase
1.18.1.2
1e6e 3.40.50.720
0.33890Compare
M0090 adenosylhomocysteinase
3.3.1.1
1b3r 3.40.50.720
0.56960.1384Compare
M0226 UDP-sulfoquinovose synthase
3.13.1.1
1qrr 3.40.50.720
0.51940.1445Compare
M0228 dTDP-glucose 4,6-dehydratase
4.2.1.46
1bxk 3.40.50.720
0.50580Compare
M0188 UDP-glucose 4-epimerase
5.1.3.2
1xel 3.40.50.720
0.34480.2144Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.40.50.720


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

GOA logo
catalytic activity (molecular function)
D-amino-acid oxidase activity (molecular function)
binding (molecular function)
peroxisome (cellular component)
metabolic process (biological process)
oxidoreductase activity (molecular function)
oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (molecular function)
oxidation-reduction process (biological process)
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