DB code: D00494

CATH domain 3.40.50.720 : Rossmann fold Catalytic domain
3.30.9.10 : D-Amino Acid Oxidase; Chain A, domain 2
E.C. 1.4.3.3
CSA 1c0k
M-CSA 1c0k
MACiE M0110

CATH domain Related DB codes (homologues)
3.40.50.720 : Rossmann fold S00543 S00551 S00552 S00553 S00602 S00604 S00605 S00608 S00610 S00625 S00319 S00328 S00329 S00330 S00331 S00332 D00456 D00457 D00458 S00324 S00320 S00325 S00326 S00327 D00459 S00335 S00336 S00334 T00219 S00339 D00513 D00001 D00002 D00003 D00005 D00007 D00008 D00010 D00012 D00017 D00018 D00023 D00027 D00028 D00031 D00032 D00033 D00034 D00035 D00037 D00048 D00071 D00476 D00481 D00482 D00490 D00492 D00545 D00601 D00603 D00604 D00605 D00615 D00845 D00857 D00858 M00161 M00171 M00210 T00002 T00010 T00011 T00015 T00227 T00247 T00408 T00414 D00827 D00262 D00274 D00275 M00035 T00109
3.30.9.10 : D-Amino Acid Oxidase; Chain A, domain 2 D00037 D00041 D00064 T00025

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P80324 D-amino-acid oxidase
DAAO
DAMOX
DAO
EC 1.4.3.3
PF01266 (DAO)
[Graphical View]

KEGG enzyme name
D-amino-acid oxidase
ophio-amino-acid oxidase
L-amino acid:O2 oxidoreductase
new yellow enzyme

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P80324 OXDA_RHOTO A D-amino acid + H(2)O + O(2) = a 2-oxo acid + NH(3) + H(2)O(2). Homodimer. Peroxisome (Potential). FAD.

KEGG Pathways
Map code Pathways E.C.
MAP00260 Glycine, serine and threonine metabolism
MAP00311 Penicillin and cephalosporin biosynthesis
MAP00330 Arginine and proline metabolism
MAP00472 D-Arginine and D-ornithine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00016 C00405 C00001 C00007 C00161 C00014 C00027
E.C.
Compound FAD D-Amino acid H2O O2 2-Oxo acid NH3 H2O2 Imino acid
Type amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotide amino acids H2O others carbohydrate,carboxyl group amine group,organic ion others
ChEBI 16238
15377
15379
26689
27140
16134
16240
PubChem 643975
22247451
962
977
222
22326046
784
1c0iA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound Unbound
1c0kA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound Unbound
1c0lA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound Unbound
1c0pA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound Unbound
1c0iA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:BE2_1364
1c0kA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:LAC Unbound Unbound Unbound Unbound Unbound
1c0lA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:FLA Unbound Unbound Unbound Unbound Unbound
1c0pA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:DAL Unbound Unbound Unbound Bound:PER Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P00371 & literature [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1c0iA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 1335 SER 1335
1c0kA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 1335 SER 1335
1c0lA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 1335 SER 1335
1c0pA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 1335 SER 1335
1c0iA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1c0kA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1c0lA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1c0pA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[9]
Scheme 1, Scheme 2, Scheme 3
[11]
Fig.7, p.618-619
[13]
p.15
[15]
FIG.5, p.7498-7499
[16]
p.5858-5859
[18]
Fig.1, p.804-806
[19]
Fig.6, Fig.7, p.829-832
[22]
Scheme 2, p.1741-1744
[23]
[24]
Scheme 2
[26]
Fig.6, p.12466-12468
[28]
Fig.1, p.14120-14121
[29]
p.540-541, p.542-544
[30]
Scheme 1, Scheme 3, p.29-31

References
[1]
Resource
Comments
Medline ID
PubMed ID 20559
Journal Med J Osaka Univ
Year 1976
Volume 27
Pages 33-46
Authors Horiike K, Shiga K, Nishina Y, Yamano T
Title pH dependence of catalysis of the monomer of hog kidney D-amino acid oxidase.
Related PDB
Related UniProtKB
[2]
Resource
Comments PRELIMINARY STUDIES ON ACTIVE SITE
Medline ID 82120157
PubMed ID 6120171
Journal J Biol Chem
Year 1982
Volume 257
Pages 1937-44
Authors Swenson RP, Williams CH Jr, Massey V
Title Chemical modification of D-amino acid oxidase. Amino acid sequence of the tryptic peptides containing tyrosine and lysine residues modified by fluorodinitrobenzene.
Related PDB
Related UniProtKB P00371
[3]
Resource
Comments PRELIMINARY STUDIES ON ACTIVE SITE
Medline ID 83082913
PubMed ID 6129252
Journal J Biol Chem
Year 1983
Volume 258
Pages 497-502
Authors Swenson RP, Williams CH Jr, Massey V
Title Identification of the histidine residue in D-amino acid oxidase that is covalently modified during inactivation by 5-dimethylaminonaphthalene-1-sulfonyl chloride.
Related PDB
Related UniProtKB P00371
[4]
Resource
Comments MUTAGENESIS OF Y-55/M-110/H-217 TO SHOW THEY ARE NOT IN ACTIVE SITE
Medline ID 8900569
PubMed ID 2901989
Journal FEBS Lett
Year 1988
Volume 238
Pages 269-72
Authors Watanabe F, Fukui K, Momoi K, Miyake Y
Title Effect of site-specific mutagenesis of tyrosine-55, methionine-110 and histidine-217 in porcine kidney D-amino acid oxidase on its catalytic function.
Related PDB
Related UniProtKB P00371
[5]
Resource
Comments
Medline ID
PubMed ID 2907883
Journal Int J Biochem
Year 1988
Volume 20
Pages 1235-8
Authors Nagata Y, Shimojo T, Akino T
Title Two spectrophotometric assays for D-amino acid oxidase: for the study of distribution patterns.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2570065
Journal J Biochem (Tokyo)
Year 1989
Volume 105
Pages 1024-9
Authors Watanabe F, Fukui K, Momoi K, Miyake Y
Title Site-specific mutagenesis of lysine-204, tyrosine-224, tyrosine-228, and histidine-307 of porcine kidney D-amino acid oxidase and the implications as to its catalytic function.
Related PDB
Related UniProtKB
[7]
Resource
Comments ACTIVE SITES TYR-228 AND HIS-307
Medline ID 91201275
PubMed ID 1673125
Journal J Biochem (Tokyo)
Year 1991
Volume 109
Pages 171-7
Authors Miyano M, Fukui K, Watanabe F, Takahashi S, Tada M, Kanashiro M, Miyake Y
Title Studies on Phe-228 and Leu-307 recombinant mutants of porcine kidney D-amino acid oxidase: expression, purification, and characterization.
Related PDB
Related UniProtKB P00371
[8]
Resource
Comments
Medline ID
PubMed ID 1351830
Journal Comp Biochem Physiol B
Year 1992
Volume 101
Pages 509-11
Authors Brachet P, Puigserver A
Title Regional differences for the D-amino acid oxidase-catalysed oxidation of D-methionine in chicken small intestine.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 7908225
Journal Biochemistry
Year 1994
Volume 33
Pages 4001-7
Authors Denu JM, Fitzpatrick PF
Title Intrinsic primary, secondary, and solvent kinetic isotope effects on the reductive half-reaction of D-amino acid oxidase: evidence against a concerted mechanism.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 7989339
Journal J Biol Chem
Year 1994
Volume 269
Pages 31666-73
Authors Pollegioni L, Fukui K, Massey V
Title Studies on the kinetic mechanism of pig kidney D-amino acid oxidase by site-directed mutagenesis of tyrosine 224 and tyrosine 228.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 8690726
Journal J Biochem (Tokyo)
Year 1995
Volume 118
Pages 614-20
Authors Nishina Y, Sato K, Miura R, Shiga K
Title Structures of charge-transfer complexes of flavoenzyme D-amino acid oxidase: a study by resonance Raman spectroscopy and extended Huckel molecular orbital method.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 8681967
Journal Eur J Biochem
Year 1996
Volume 238
Pages 519-28
Authors Stocker A, Hecht HJ, Buckmann AF
Title Synthesis, characterization and preliminary crystallographic data of N6-(6-carbamoylhexyl)-FAD-D-amino-acid oxidase from pig kidney, a semi-synthetic oxidase.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY
Medline ID 97018220
PubMed ID 8864836
Journal J Biochem (Tokyo)
Year 1996
Volume 120
Pages 14-7
Authors Mizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R
Title Three-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 A resolution.
Related PDB 1aa8 1ve9
Related UniProtKB P00371
[14]
Resource
Comments
Medline ID
PubMed ID 8827446
Journal J Biochem (Tokyo)
Year 1996
Volume 119
Pages 1114-7
Authors Setoyama C, Miura R, Nishina Y, Shiga K, Mizutani H, Miyahara I, Hirotsu K
Title Crystallization of expressed porcine kidney D-amino acid oxidase and preliminary X-ray crystallographic characterization.
Related PDB
Related UniProtKB
[15]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID 96353844
PubMed ID 8755502
Journal Proc Natl Acad Sci U S A
Year 1996
Volume 93
Pages 7496-501
Authors Mattevi A, Vanoni MA, Todone F, Rizzi M, Teplyakov A, Coda A, Bolognesi M, Curti B
Title Crystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2.
Related PDB 1kif
Related UniProtKB P00371
[16]
Resource
Comments X-RAY CRYSTALLOGRAPHY
Medline ID 97297794
PubMed ID 9153426
Journal Biochemistry
Year 1997
Volume 36
Pages 5853-60
Authors Todone F, Vanoni MA, Mozzarelli A, Bolognesi M, Coda A, Curti B, Mattevi A
Title Active site plasticity in D-amino acid oxidase: a crystallographic analysis.
Related PDB 1ddo 1dao
Related UniProtKB P00371
[17]
Resource
Comments
Medline ID
PubMed ID 9153402
Journal Biochemistry
Year 1997
Volume 36
Pages 5624-32
Authors Vanoni MA, Cosma A, Mazzeo D, Mattevi A, Todone F, Curti B
Title Limited proteolysis and X-ray crystallography reveal the origin of substrate specificity and of the rate-limiting product release during oxidation of D-amino acids catalyzed by mammalian D-amino acid oxidase.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 9434899
Journal Curr Opin Struct Biol
Year 1997
Volume 7
Pages 804-10
Authors Mattevi A, Vanoni MA, Curti B
Title Structure of D-amino acid oxidase: new insights from an old enzyme.
Related PDB
Related UniProtKB
[19]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9399588
Journal J Biochem (Tokyo)
Year 1997
Volume 122
Pages 825-33
Authors Miura R, Setoyama C, Nishina Y, Shiga K, Mizutani H, Miyahara I, Hirotsu K
Title Structural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex.
Related PDB 1an9
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 9268372
Journal J Biol Chem
Year 1997
Volume 272
Pages 22248-52
Authors Raibekas AA, Massey V
Title Glycerol-assisted restorative adjustment of flavoenzyme conformation perturbed by site-directed mutagenesis.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 10427728
Journal FEMS Microbiol Lett
Year 1999
Volume 176
Pages 443-8
Authors Lin LL, Wang WC, Ju SS, Chien HR, Hsu WH
Title The role of a conserved histidine residue, His324, in Trigonopsis variabilis D-amino acid oxidase.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 11130179
Journal Cell Mol Life Sci
Year 2000
Volume 57
Pages 1732-47
Authors Pilone MS
Title D-Amino acid oxidase: new findings.
Related PDB
Related UniProtKB
[23]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10876160
Journal J Biochem (Tokyo)
Year 2000
Volume 128
Pages 73-81
Authors Mizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R
Title Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin.
Related PDB 1evi
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 10920257
Journal J Biochem (Tokyo)
Year 2000
Volume 128
Pages 213-23
Authors Nishina Y, Sato K, Miura R, Shiga K
Title Substrate recognition and activation mechanism of D-amino acid oxidase: a study using substrate analogs.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 10716694
Journal Proc Natl Acad Sci U S A
Year 2000
Volume 97
Pages 3089-93
Authors Raibekas AA, Fukui K, Massey V
Title Design and properties of human D-amino acid oxidase with covalently attached flavin.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 11070076
Journal Proc Natl Acad Sci U S A
Year 2000
Volume 97
Pages 12463-8
Authors Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S
Title The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.
Related PDB 1c0k 1c0l 1c0p
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 11686926
Journal J Biochem (Tokyo)
Year 2001
Volume 130
Pages 637-47
Authors Nishina Y, Sato K, Shi R, Setoyama C, Miura R, Shiga K
Title On the ligands in charge-transfer complexes of porcine kidney flavoenzyme D-amino acid oxidase in three redox states: a resonance Raman study.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 12450374
Journal Biochemistry
Year 2002
Volume 41
Pages 14111-21
Authors Tilocca A, Gamba A, Vanoni MA, Fois E
Title First-principles molecular dynamics investigation of the D-amino acid oxidative half-reaction catalyzed by the flavoenzyme D-amino acid oxidase.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 12445787
Journal J Mol Biol
Year 2002
Volume 324
Pages 535-46
Authors Pollegioni L, Diederichs K, Molla G, Umhau S, Welte W, Ghisla S, Pilone MS
Title Yeast D-amino acid oxidase: structural basis of its catalytic properties.
Related PDB 1c0i
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 15450847
Journal Biochim Biophys Acta
Year 2004
Volume 1702
Pages 19-32
Authors Boselli A, Piubelli L, Molla G, Sacchi S, Pilone MS, Ghisla S, Pollegioni L
Title On the mechanism of Rhodotorula gracilis D-amino acid oxidase: role of the active site serine 335.
Related PDB
Related UniProtKB

Comments
Although the first domain of this enzyme is classified in CATH 3.40.50.720, it should be homologous to sarcosine oxidase (E.C. 1.5.3.1; D00041 in EzCatDB), and is re-classified into CATH 3.50.50.60 in this database.
Although this enzyme is homologous to a mammalian counterpart (D00037 in EzCatDB), a set of catalytic residues is slightly different from the counterpart. The sidechain of Ser335 plays a catalytic role as the counterpart of corresponding Tyr224 in the mammalian enzyme (see D00037) (see [15] & [26]).
According to the literature [22], this enzyme catalyzes the following reactions:
(A) Hydride transfer from D-amino acid to FAD, giving imino acid and FADH2 (reductive half-reaction).
(B) Hydride transfer from FADH2 to O2, giving FAD and H2O2 (oxidative half-reaction).
(C) Exchange of double-bonded atoms of the imino acid (Schiff-base deformation by water)

Created Updated
2005-01-25 2009-03-16