EzCatDB: D00041
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DB codeD00041
CATH domainDomain 13.50.50.60 : FAD/NAD(P)-binding domainCatalytic domain
Domain 23.30.9.10 : D-Amino Acid Oxidase; Chain A, domain 2Catalytic domain
E.C.1.5.3.1
CSA1b3m

CATH domainRelated DB codes (homologues)
3.30.9.10 : D-Amino Acid Oxidase; Chain A, domain 2D00037,D00064,D00494,T00025
3.50.50.60 : FAD/NAD(P)-binding domainM00163,D00015,D00042,D00045,D00064,D00071,T00004,T00015,T00017,T00025,T00211,T00213,T00233,T00242

Enzyme Name
UniProtKBKEGG

P40859
Protein nameMonomeric sarcosine oxidasesarcosine oxidase
SynonymsMSOX
EC 1.5.3.1
PfamPF01266 (DAO)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00260Glycine, serine and threonine metabolism

UniProtKB:Accession NumberP40859
Entry nameMSOX_BACB0
ActivitySarcosine + H(2)O + O(2) = glycine + formaldehyde + H(2)O(2).
SubunitMonomer.
Subcellular locationCytoplasm.
CofactorBinds 1 FAD per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00016C00213C00001C00007C00037C00067C00027
CompoundFADSarcosineH2OO2GlycineFormaldehydeH2O2
Typeamide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotideamino acidsH2Oothersamino acidscarbohydrateothers
ChEBI16238
15611
57433
15377
27140
26689
15379
15428
57305
16842
16240
PubChem643975
7311726
1088
962
22247451
977
750
5257127
712
784
22326046
               
1b3mA01Bound:FADUnbound UnboundUnboundUnboundUnbound
1b3mB01Bound:FADUnbound UnboundUnboundUnboundUnbound
1el5A01Bound:FADAnalogue:DMG UnboundUnboundUnboundUnbound
1el5B01Bound:FADAnalogue:DMG UnboundUnboundUnboundUnbound
1el7A01Bound:FADAnalogue:MTD UnboundUnboundUnboundUnbound
1el7B01Bound:FADAnalogue:MTD UnboundUnboundUnboundUnbound
1el8A01Bound:FADUnbound UnboundAnalogue:MSFUnboundUnbound
1el8B01Bound:FADUnbound UnboundAnalogue:MSFUnboundUnbound
1el9A01Bound:FADAnalogue:MTG UnboundUnboundUnboundUnbound
1el9B01Bound:FADAnalogue:MTG UnboundUnboundUnboundUnbound
1eliA01Bound:FADAnalogue:PYC UnboundUnboundUnboundUnbound
1eliB01Bound:FADAnalogue:PYC UnboundUnboundUnboundUnbound
1l9cA01Bound:FADUnbound UnboundUnboundUnboundUnbound
1l9cB01Bound:FADUnbound UnboundUnboundUnboundUnbound
1l9dA01Bound:FADAnalogue:PYC UnboundUnboundUnboundUnbound
1l9dB01Bound:FADAnalogue:PYC UnboundUnboundUnboundUnbound
1l9eA01Bound:FADUnbound UnboundUnboundUnboundUnbound
1l9eB01Bound:FADUnbound UnboundUnboundUnboundUnbound
1l9fA01Bound:FADUnbound UnboundUnboundUnboundUnbound
1l9fB01Bound:FADUnbound UnboundUnboundUnboundUnbound
1b3mA02UnboundUnbound UnboundUnboundUnboundUnbound
1b3mB02UnboundUnbound UnboundUnboundUnboundUnbound
1el5A02UnboundUnbound UnboundUnboundUnboundUnbound
1el5B02UnboundUnbound UnboundUnboundUnboundUnbound
1el7A02UnboundUnbound UnboundUnboundUnboundUnbound
1el7B02UnboundUnbound UnboundUnboundUnboundUnbound
1el8A02UnboundUnbound UnboundUnboundUnboundUnbound
1el8B02UnboundUnbound UnboundUnboundUnboundUnbound
1el9A02UnboundUnbound UnboundUnboundUnboundUnbound
1el9B02UnboundUnbound UnboundUnboundUnboundUnbound
1eliA02UnboundUnbound UnboundUnboundUnboundUnbound
1eliB02UnboundUnbound UnboundUnboundUnboundUnbound
1l9cA02UnboundUnbound UnboundUnboundUnboundUnbound
1l9cB02UnboundUnbound UnboundUnboundUnboundUnbound
1l9dA02UnboundUnbound UnboundUnboundUnboundUnbound
1l9dB02UnboundUnbound UnboundUnboundUnboundUnbound
1l9eA02UnboundUnbound UnboundUnboundUnboundUnbound
1l9eB02UnboundUnbound UnboundUnboundUnboundUnbound
1l9fA02UnboundUnbound UnboundUnboundUnboundUnbound
1l9fB02UnboundUnbound UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [8]
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
            
1b3mA01HIS 45;ARG 49
 
 
 
1b3mB01HIS 45;ARG 49
 
 
 
1el5A01HIS 45;ARG 49
 
 
 
1el5B01HIS 45;ARG 49
 
 
 
1el7A01HIS 45;ARG 49
 
 
 
1el7B01HIS 45;ARG 49
 
 
 
1el8A01HIS 45;ARG 49
 
 
 
1el8B01HIS 45;ARG 49
 
 
 
1el9A01HIS 45;ARG 49
 
MSE 14;MSE 16;MSE 201(selenide)
 
1el9B01HIS 45;ARG 49
 
MSE 14;MSE 16;MSE 201(selenide)
 
1eliA01HIS 45;ARG 49
 
MSE 14;MSE 16;MSE 201(selenide)
 
1eliB01HIS 45;ARG 49
 
MSE 14;MSE 16;MSE 201(selenide)
 
1l9cA01HIS 45;ARG 49
 
 
 
1l9cB01HIS 45;ARG 49
 
 
 
1l9dA01HIS 45;ARG 49
 
 
 
1l9dB01HIS 45;ARG 49
 
 
 
1l9eA01HIS 45;ARG 49
 
 
 
1l9eB01HIS 45;ARG 49
 
 
 
1l9fA01HIS 45;ARG 49
 
 
 
1l9fB01HIS 45;ARG 49
 
 
 
1b3mA02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1b3mB02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1el5A02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1el5B02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1el7A02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1el7B02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1el8A02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1el8B02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1el9A02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
MSE 105;MSE 245;MSE 302;MSE 316(selenide)
 
1el9B02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
MSE 105;MSE 245;MSE 302;MSE 316(selenide)
 
1eliA02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
MSE 105;MSE 245;MSE 302;MSE 316(selenide)
 
1eliB02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
MSE 105;MSE 245;MSE 302;MSE 316(selenide)
 
1l9cA02       ;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
mutant H269N
1l9cB02       ;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
mutant H269N
1l9dA02       ;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
mutant H269N
1l9dB02       ;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
mutant H269N
1l9eA02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1l9eB02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1l9fA02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 
1l9fB02HIS 269;CYS 315
CYS 315(S-8alpha-FAD cysteine)
 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[10]Fig.6, p.339
[12]Scheme 1
[15]

[17]Scheme 2

references
[1]
PubMed ID3427080
JournalBiochemistry
Year1987
Volume26
Pages7391-5
AuthorsKvalnes-Krick K, Jorns MS
TitleInteraction of tetrahydrofolate and other folate derivatives with bacterial sarcosine oxidase.
[2]
PubMed ID1657156
JournalBiochemistry
Year1991
Volume30
Pages10980-6
AuthorsAli SN, Zeller HD, Calisto MK, Jorns MS
TitleKinetics of electron entry, exit, and interflavin electron transfer during catalysis by sarcosine oxidase.
[3]
PubMed ID1939012
JournalJ Biochem (Tokyo)
Year1991
Volume109
Pages909-17
AuthorsSuzuki H, Kawamura-Konishi Y
TitleCysteine residues in the active site of Corynebacterium sarcosine oxidase.
[4]
PubMed ID7887617
JournalAppl Environ Microbiol
Year1995
Volume61
Pages367-70
AuthorsNishiya Y, Zuihara S, Imanaka T
TitleActive site analysis and stabilization of sarcosine oxidase by the substitution of cysteine residues.
[5]
PubMed ID8779579
JournalAppl Environ Microbiol
Year1996
Volume62
Pages2405-10
AuthorsNishiya Y, Imanaka T
TitleAnalysis of interaction between the Arthrobacter sarcosine oxidase and the coenzyme flavin adenine dinucleotide by site-directed mutagenesis.
[6]
PubMed ID8611516
JournalBiochemistry
Year1996
Volume35
Pages5292-9
AuthorsWillie A, Edmondson DE, Jorns MS
TitleSarcosine oxidase contains a novel covalently bound FMN.
[7]
PubMed ID9356299
JournalJ Struct Biol
Year1997
Volume120
Pages109-11
AuthorsIchikawa T, Sasaki H, Koike H, Nishiyama M, Koyama Y, Tanokura M
TitleCrystallization and preliminary crystallographic analysis of the sarcosine oxidase from Bacillus sp. NS-129.
[8]
PubMed ID9485355
JournalBiochemistry
Year1998
Volume37
Pages2089-95
AuthorsChlumsky LJ, Sturgess AW, Nieves E, Jorns MS
TitleIdentification of the covalent flavin attachment site in sarcosine oxidase.
[9]
CommentsCHARACTERIZATION, SEQUENCE OF 313-319, AND MASS SPECTROMETRY
Medline ID99238335
PubMed ID10220347
JournalBiochemistry
Year1999
Volume38
Pages5588-95
AuthorsWagner MA, Khanna P, Jorns MS
TitleStructure of the flavocoenzyme of two homologous amine oxidases: monomeric sarcosine oxidase and N-methyltryptophan oxidase.
Related UniProtKBP40859
[10]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
Medline ID99197298
PubMed ID10368302
JournalStructure Fold Des
Year1999
Volume7
Pages331-45
AuthorsTrickey P, Wagner MA, Jorns MS, Mathews FS
TitleMonomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.
Related PDB1b3m,1l9f
Related UniProtKBP40859
[11]
CommentsCHARACTERIZATION
Medline ID20374561
PubMed ID10913293
JournalBiochemistry
Year2000
Volume39
Pages8825-9
AuthorsWagner MA, Jorns MS
TitleMonomeric sarcosine oxidase: 2. Kinetic studies with sarcosine, alternate substrates, and a substrate analogue.
Related UniProtKBP40859
[12]
CommentsX-ray crystallography
PubMed ID10913292
JournalBiochemistry
Year2000
Volume39
Pages8813-24
AuthorsWagner MA, Trickey P, Chen ZW, Mathews FS, Jorns MS
TitleMonomeric sarcosine oxidase: 1. Flavin reactivity and active site binding determinants.
Related PDB1el5,1el7,1el8,1el9,1eli
[13]
CommentsCHARACTERIZATION
Medline ID20541388
PubMed ID11087383
JournalBiochemistry
Year2000
Volume39
Pages14341-7
AuthorsZhao G, Qu J, Davis FA, Jorns MS
TitleInactivation of monomeric sarcosine oxidase by reaction with N-(cyclopropyl)glycine.
[14]
PubMed ID11035956
JournalProtein Expr Purif
Year2000
Volume20
Pages95-7
AuthorsNishiya Y
TitleA mutant sarcosine oxidase in which activity depends on flavin adenine dinucleotide.
[15]
CommentsX-ray crystallography
PubMed ID12146941
JournalBiochemistry
Year2002
Volume41
Pages9751-64
AuthorsZhao G, Song H, Chen ZW, Mathews FS, Jorns MS
TitleMonomeric sarcosine oxidase: role of histidine 269 in catalysis.
Related PDB1l9c,1l9d,1l9e
[16]
PubMed ID12084049
JournalEur J Biochem
Year2002
Volume269
Pages3096-102
AuthorsSutcliffe MJ, Scrutton NS
TitleA new conceptual framework for enzyme catalysis. Hydrogen tunnelling coupled to enzyme dynamics in flavoprotein and quinoprotein enzymes.
[17]
PubMed ID12549903
JournalBiochemistry
Year2003
Volume42
Pages864-9
AuthorsKhanna P, Jorns MS
TitleTautomeric rearrangement of a dihydroflavin bound to monomeric sarcosine oxidase or N-methyltryptophan oxidase.
[18]
PubMed ID15240125
JournalBiochem Biophys Res Commun
Year2004
Volume320
Pages846-51
AuthorsMukouyama EB, Oguchi M, Kodera Y, Maeda T, Suzuki H
TitleLow pKa lysine residues at the active site of sarcosine oxidase from Corynebacterium sp. U-96.

comments
This enzyme catalyzes several reactions as follows:
(A) Oxidation of sarcosine by FAD, giving a Schiff-base intermediate and FADH2.
(B) Exchange of double-bonded atoms (Schiff-base) by hydration, giving formaldehyde and glycine.
(C) Hydride transfer from FADH2 to O2 (Re-oxidation of FAD by O2, releasing H2O2).

createdupdated
2004-03-242009-02-26
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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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