EzCatDB: D00494

DB codeD00494
CATH domainDomain 13.40.50.720Catalytic domain
Domain 23.30.9.10
E.C.1.4.3.3
CSA1c0k
MACiEM0110

CATH domainRelated DB codes (homologues)
3.30.9.10D00037,D00041,D00064,T00025
3.40.50.720S00543,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

Enzyme Name
Swiss-protKEGG

P80324
Protein nameD-amino-acid oxidaseD-amino-acid oxidase
ophio-amino-acid oxidase
L-amino acid:O2 oxidoreductase
new yellow enzyme
SynonymsDAMOX
DAAO
DAO
EC 1.4.3.3

KEGG pathways
MAP codePathways
MAP00260Glycine, serine and threonine metabolism
MAP00311Penicillin and cephalosporin biosynthesis
MAP00330Arginine and proline metabolism
MAP00472D-Arginine and D-ornithine metabolism

Swiss-prot:Accession NumberP80324
Entry nameOXDA_RHOTO
ActivityA D-amino acid + H(2)O + O(2) = a 2-oxo acid + NH(3) + H(2)O(2).
SubunitHomodimer.
Subcellular locationPeroxisome (Potential).
CofactorFAD.


CofactorsSubstratesProductsintermediates
KEGG-idC00016C00405C00001C00007C00161C00014C00027
CompoundFADD-Amino acidH2OO22-Oxo acidNH3H2O2Imino acid
Typeamide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotideamino acidsH2Ootherscarbohydrate,carboxyl groupamine group,organic ionothers
1c0iA01Bound:FADUnbound
UnboundUnboundUnboundUnboundUnbound
1c0kA01Bound:FADUnbound
UnboundUnboundUnboundUnboundUnbound
1c0lA01Bound:FADUnbound
UnboundUnboundUnboundUnboundUnbound
1c0pA01Bound:FADUnbound
UnboundUnboundUnboundUnboundUnbound
1c0iA02UnboundUnbound
UnboundUnboundUnboundUnboundIntermediate-analogue:BE2 1364
1c0kA02UnboundAnalogue:LAC
UnboundUnboundUnboundUnboundUnbound
1c0lA02UnboundAnalogue:FLA
UnboundUnboundUnboundUnboundUnbound
1c0pA02UnboundBound:DAL
UnboundUnboundUnboundBound:PERUnbound

Active-site residues
resource
Swiss-prot;P00371 & literature [6]
pdbCatalytic residuesMain-chain involved in catalysis
1c0iA01SER 1335
SER 1335
1c0kA01SER 1335
SER 1335
1c0lA01SER 1335
SER 1335
1c0pA01SER 1335
SER 1335
1c0iA02        

1c0kA02        

1c0lA02        

1c0pA02        


References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID20559
JournalMed J Osaka Univ
Year1976
Volume27
Pages33-46
AuthorsHoriike K, Shiga K, Nishina Y, Yamano T
TitlepH dependence of catalysis of the monomer of hog kidney D-amino acid oxidase.
[2]
CommentsPRELIMINARY STUDIES ON ACTIVE SITE
Medline ID82120157
PubMed ID6120171
JournalJ Biol Chem
Year1982
Volume257
Pages1937-44
AuthorsSwenson RP, Williams CH Jr, Massey V
TitleChemical modification of D-amino acid oxidase. Amino acid sequence of the tryptic peptides containing tyrosine and lysine residues modified by fluorodinitrobenzene.
Related Swiss-protP00371
[3]
CommentsPRELIMINARY STUDIES ON ACTIVE SITE
Medline ID83082913
PubMed ID6129252
JournalJ Biol Chem
Year1983
Volume258
Pages497-502
AuthorsSwenson RP, Williams CH Jr, Massey V
TitleIdentification of the histidine residue in D-amino acid oxidase that is covalently modified during inactivation by 5-dimethylaminonaphthalene-1-sulfonyl chloride.
Related Swiss-protP00371
[4]
CommentsMUTAGENESIS OF Y-55/M-110/H-217 TO SHOW THEY ARE NOT IN ACTIVE SITE
Medline ID8900569
PubMed ID2901989
JournalFEBS Lett
Year1988
Volume238
Pages269-72
AuthorsWatanabe F, Fukui K, Momoi K, Miyake Y
TitleEffect of site-specific mutagenesis of tyrosine-55, methionine-110 and histidine-217 in porcine kidney D-amino acid oxidase on its catalytic function.
Related Swiss-protP00371
[5]
PubMed ID2907883
JournalInt J Biochem
Year1988
Volume20
Pages1235-8
AuthorsNagata Y, Shimojo T, Akino T
TitleTwo spectrophotometric assays for D-amino acid oxidase: for the study of distribution patterns.
[6]
PubMed ID2570065
JournalJ Biochem (Tokyo)
Year1989
Volume105
Pages1024-9
AuthorsWatanabe F, Fukui K, Momoi K, Miyake Y
TitleSite-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.
[7]
CommentsACTIVE SITES TYR-228 AND HIS-307
Medline ID91201275
PubMed ID1673125
JournalJ Biochem (Tokyo)
Year1991
Volume109
Pages171-7
AuthorsMiyano M, Fukui K, Watanabe F, Takahashi S, Tada M, Kanashiro M, Miyake Y
TitleStudies on Phe-228 and Leu-307 recombinant mutants of porcine kidney D-amino acid oxidase: expression, purification, and characterization.
Related Swiss-protP00371
[8]
PubMed ID1351830
JournalComp Biochem Physiol B
Year1992
Volume101
Pages509-11
AuthorsBrachet P, Puigserver A
TitleRegional differences for the D-amino acid oxidase-catalysed oxidation of D-methionine in chicken small intestine.
[9]
PubMed ID7908225
JournalBiochemistry
Year1994
Volume33
Pages4001-7
AuthorsDenu JM, Fitzpatrick PF
TitleIntrinsic primary, secondary, and solvent kinetic isotope effects on the reductive half-reaction of D-amino acid oxidase: evidence against a concerted mechanism.
[10]
PubMed ID7989339
JournalJ Biol Chem
Year1994
Volume269
Pages31666-73
AuthorsPollegioni L, Fukui K, Massey V
TitleStudies on the kinetic mechanism of pig kidney D-amino acid oxidase by site-directed mutagenesis of tyrosine 224 and tyrosine 228.
[11]
PubMed ID8690726
JournalJ Biochem (Tokyo)
Year1995
Volume118
Pages614-20
AuthorsNishina Y, Sato K, Miura R, Shiga K
TitleStructures of charge-transfer complexes of flavoenzyme D-amino acid oxidase: a study by resonance Raman spectroscopy and extended Huckel molecular orbital method.
[12]
PubMed ID8681967
JournalEur J Biochem
Year1996
Volume238
Pages519-28
AuthorsStocker A, Hecht HJ, Buckmann AF
TitleSynthesis, characterization and preliminary crystallographic data of N6-(6-carbamoylhexyl)-FAD-D-amino-acid oxidase from pig kidney, a semi-synthetic oxidase.
[13]
CommentsX-RAY CRYSTALLOGRAPHY
Medline ID97018220
PubMed ID8864836
JournalJ Biochem (Tokyo)
Year1996
Volume120
Pages14-7
AuthorsMizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R
TitleThree-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 A resolution.
Related PDB1aa8,1ve9
Related Swiss-protP00371
[14]
PubMed ID8827446
JournalJ Biochem (Tokyo)
Year1996
Volume119
Pages1114-7
AuthorsSetoyama C, Miura R, Nishina Y, Shiga K, Mizutani H, Miyahara I, Hirotsu K
TitleCrystallization of expressed porcine kidney D-amino acid oxidase and preliminary X-ray crystallographic characterization.
[15]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID96353844
PubMed ID8755502
JournalProc Natl Acad Sci U S A
Year1996
Volume93
Pages7496-501
AuthorsMattevi A, Vanoni MA, Todone F, Rizzi M, Teplyakov A, Coda A, Bolognesi M, Curti B
TitleCrystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2.
Related PDB1kif
Related Swiss-protP00371
[16]
CommentsX-RAY CRYSTALLOGRAPHY
Medline ID97297794
PubMed ID9153426
JournalBiochemistry
Year1997
Volume36
Pages5853-60
AuthorsTodone F, Vanoni MA, Mozzarelli A, Bolognesi M, Coda A, Curti B, Mattevi A
TitleActive site plasticity in D-amino acid oxidase: a crystallographic analysis.
Related PDB1ddo,1dao
Related Swiss-protP00371
[17]
PubMed ID9153402
JournalBiochemistry
Year1997
Volume36
Pages5624-32
AuthorsVanoni MA, Cosma A, Mazzeo D, Mattevi A, Todone F, Curti B
TitleLimited 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.
[18]
PubMed ID9434899
JournalCurr Opin Struct Biol
Year1997
Volume7
Pages804-10
AuthorsMattevi A, Vanoni MA, Curti B
TitleStructure of D-amino acid oxidase: new insights from an old enzyme.
[19]
CommentsX-ray crystallography
PubMed ID9399588
JournalJ Biochem (Tokyo)
Year1997
Volume122
Pages825-33
AuthorsMiura R, Setoyama C, Nishina Y, Shiga K, Mizutani H, Miyahara I, Hirotsu K
TitleStructural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex.
Related PDB1an9
[20]
PubMed ID9268372
JournalJ Biol Chem
Year1997
Volume272
Pages22248-52
AuthorsRaibekas AA, Massey V
TitleGlycerol-assisted restorative adjustment of flavoenzyme conformation perturbed by site-directed mutagenesis.
[21]
PubMed ID10427728
JournalFEMS Microbiol Lett
Year1999
Volume176
Pages443-8
AuthorsLin LL, Wang WC, Ju SS, Chien HR, Hsu WH
TitleThe role of a conserved histidine residue, His324, in Trigonopsis variabilis D-amino acid oxidase.
[22]
PubMed ID11130179
JournalCell Mol Life Sci
Year2000
Volume57
Pages1732-47
AuthorsPilone MS
TitleD-Amino acid oxidase: new findings.
[23]
CommentsX-ray crystallography
PubMed ID10876160
JournalJ Biochem (Tokyo)
Year2000
Volume128
Pages73-81
AuthorsMizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R
TitleThree-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 PDB1evi
[24]
PubMed ID10920257
JournalJ Biochem (Tokyo)
Year2000
Volume128
Pages213-23
AuthorsNishina Y, Sato K, Miura R, Shiga K
TitleSubstrate recognition and activation mechanism of D-amino acid oxidase: a study using substrate analogs.
[25]
PubMed ID10716694
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages3089-93
AuthorsRaibekas AA, Fukui K, Massey V
TitleDesign and properties of human D-amino acid oxidase with covalently attached flavin.
[26]
PubMed ID11070076
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages12463-8
AuthorsUmhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S
TitleThe x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.
Related PDB1c0k,1c0l,1c0p
[27]
PubMed ID11686926
JournalJ Biochem (Tokyo)
Year2001
Volume130
Pages637-47
AuthorsNishina Y, Sato K, Shi R, Setoyama C, Miura R, Shiga K
TitleOn the ligands in charge-transfer complexes of porcine kidney flavoenzyme D-amino acid oxidase in three redox states: a resonance Raman study.
[28]
PubMed ID12450374
JournalBiochemistry
Year2002
Volume41
Pages14111-21
AuthorsTilocca A, Gamba A, Vanoni MA, Fois E
TitleFirst-principles molecular dynamics investigation of the D-amino acid oxidative half-reaction catalyzed by the flavoenzyme D-amino acid oxidase.
[29]
PubMed ID12445787
JournalJ Mol Biol
Year2002
Volume324
Pages535-46
AuthorsPollegioni L, Diederichs K, Molla G, Umhau S, Welte W, Ghisla S, Pilone MS
TitleYeast D-amino acid oxidase: structural basis of its catalytic properties.
Related PDB1c0i
[30]
PubMed ID15450847
JournalBiochim Biophys Acta
Year2004
Volume1702
Pages19-32
AuthorsBoselli A, Piubelli L, Molla G, Sacchi S, Pilone MS, Ghisla S, Pollegioni L
TitleOn the mechanism of Rhodotorula gracilis D-amino acid oxidase: role of the active site serine 335.

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)

createdupdated
2005-01-252009-03-16


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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