DB code: D00041

CATH domain 3.50.50.60 : FAD/NAD(P)-binding domain Catalytic domain
3.30.9.10 : D-Amino Acid Oxidase; Chain A, domain 2 Catalytic domain
E.C. 1.5.3.1
CSA 1b3m
M-CSA 1b3m
MACiE

CATH domain Related DB codes (homologues)
3.50.50.60 : FAD/NAD(P)-binding domain M00163 D00015 D00042 D00045 D00064 D00071 T00004 T00015 T00017 T00025 T00211 T00213 T00233 T00242
3.30.9.10 : D-Amino Acid Oxidase; Chain A, domain 2 D00037 D00064 D00494 T00025

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P40859 Monomeric sarcosine oxidase
MSOX
EC 1.5.3.1
PF01266 (DAO)
[Graphical View]

KEGG enzyme name
sarcosine oxidase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P40859 MSOX_BACB0 Sarcosine + H(2)O + O(2) = glycine + formaldehyde + H(2)O(2). Monomer. Cytoplasm. Binds 1 FAD per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00260 Glycine, serine and threonine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00016 C00213 C00001 C00007 C00037 C00067 C00027
E.C.
Compound FAD Sarcosine H2O O2 Glycine Formaldehyde H2O2
Type amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotide amino acids H2O others amino acids carbohydrate others
ChEBI 16238
15611
57433
15377
15379
26689
27140
15428
57305
16842
16240
PubChem 643975
1088
7311726
22247451
962
977
5257127
750
712
22326046
784
1b3mA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound
1b3mB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound
1el5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:DMG Unbound Unbound Unbound Unbound
1el5B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:DMG Unbound Unbound Unbound Unbound
1el7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:MTD Unbound Unbound Unbound Unbound
1el7B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:MTD Unbound Unbound Unbound Unbound
1el8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Analogue:MSF Unbound Unbound
1el8B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Analogue:MSF Unbound Unbound
1el9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:MTG Unbound Unbound Unbound Unbound
1el9B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:MTG Unbound Unbound Unbound Unbound
1eliA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:PYC Unbound Unbound Unbound Unbound
1eliB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:PYC Unbound Unbound Unbound Unbound
1l9cA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound
1l9cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound
1l9dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:PYC Unbound Unbound Unbound Unbound
1l9dB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Analogue:PYC Unbound Unbound Unbound Unbound
1l9eA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound
1l9eB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound
1l9fA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound
1l9fB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound
1b3mA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1b3mB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1el5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1el5B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1el7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1el7B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1el8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1el8B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1el9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1el9B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1eliA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1eliB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l9cA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l9cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l9dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l9dB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l9eA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l9eB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l9fA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1l9fB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [8]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b3mA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1b3mB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1el5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1el5B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1el7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1el7B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1el8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1el8B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1el9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49 MSE 14;MSE 16;MSE 201(selenide)
1el9B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49 MSE 14;MSE 16;MSE 201(selenide)
1eliA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49 MSE 14;MSE 16;MSE 201(selenide)
1eliB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49 MSE 14;MSE 16;MSE 201(selenide)
1l9cA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1l9cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1l9dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1l9dB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1l9eA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1l9eB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1l9fA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1l9fB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 45;ARG 49
1b3mA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1b3mB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1el5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1el5B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1el7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1el7B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1el8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1el8B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1el9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine) MSE 105;MSE 245;MSE 302;MSE 316(selenide)
1el9B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine) MSE 105;MSE 245;MSE 302;MSE 316(selenide)
1eliA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine) MSE 105;MSE 245;MSE 302;MSE 316(selenide)
1eliB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine) MSE 105;MSE 245;MSE 302;MSE 316(selenide)
1l9cA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;CYS 315 CYS 315(S-8alpha-FAD cysteine) mutant H269N
1l9cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;CYS 315 CYS 315(S-8alpha-FAD cysteine) mutant H269N
1l9dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;CYS 315 CYS 315(S-8alpha-FAD cysteine) mutant H269N
1l9dB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;CYS 315 CYS 315(S-8alpha-FAD cysteine) mutant H269N
1l9eA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1l9eB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1l9fA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)
1l9fB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 269;CYS 315 CYS 315(S-8alpha-FAD cysteine)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[10]
Fig.6, p.339
[12]
Scheme 1
[15]
[17]
Scheme 2

References
[1]
Resource
Comments
Medline ID
PubMed ID 3427080
Journal Biochemistry
Year 1987
Volume 26
Pages 7391-5
Authors Kvalnes-Krick K, Jorns MS
Title Interaction of tetrahydrofolate and other folate derivatives with bacterial sarcosine oxidase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1657156
Journal Biochemistry
Year 1991
Volume 30
Pages 10980-6
Authors Ali SN, Zeller HD, Calisto MK, Jorns MS
Title Kinetics of electron entry, exit, and interflavin electron transfer during catalysis by sarcosine oxidase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1939012
Journal J Biochem (Tokyo)
Year 1991
Volume 109
Pages 909-17
Authors Suzuki H, Kawamura-Konishi Y
Title Cysteine residues in the active site of Corynebacterium sarcosine oxidase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7887617
Journal Appl Environ Microbiol
Year 1995
Volume 61
Pages 367-70
Authors Nishiya Y, Zuihara S, Imanaka T
Title Active site analysis and stabilization of sarcosine oxidase by the substitution of cysteine residues.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8779579
Journal Appl Environ Microbiol
Year 1996
Volume 62
Pages 2405-10
Authors Nishiya Y, Imanaka T
Title Analysis of interaction between the Arthrobacter sarcosine oxidase and the coenzyme flavin adenine dinucleotide by site-directed mutagenesis.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8611516
Journal Biochemistry
Year 1996
Volume 35
Pages 5292-9
Authors Willie A, Edmondson DE, Jorns MS
Title Sarcosine oxidase contains a novel covalently bound FMN.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9356299
Journal J Struct Biol
Year 1997
Volume 120
Pages 109-11
Authors Ichikawa T, Sasaki H, Koike H, Nishiyama M, Koyama Y, Tanokura M
Title Crystallization and preliminary crystallographic analysis of the sarcosine oxidase from Bacillus sp. NS-129.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9485355
Journal Biochemistry
Year 1998
Volume 37
Pages 2089-95
Authors Chlumsky LJ, Sturgess AW, Nieves E, Jorns MS
Title Identification of the covalent flavin attachment site in sarcosine oxidase.
Related PDB
Related UniProtKB
[9]
Resource
Comments CHARACTERIZATION, SEQUENCE OF 313-319, AND MASS SPECTROMETRY
Medline ID 99238335
PubMed ID 10220347
Journal Biochemistry
Year 1999
Volume 38
Pages 5588-95
Authors Wagner MA, Khanna P, Jorns MS
Title Structure of the flavocoenzyme of two homologous amine oxidases: monomeric sarcosine oxidase and N-methyltryptophan oxidase.
Related PDB
Related UniProtKB P40859
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
Medline ID 99197298
PubMed ID 10368302
Journal Structure Fold Des
Year 1999
Volume 7
Pages 331-45
Authors Trickey P, Wagner MA, Jorns MS, Mathews FS
Title Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.
Related PDB 1b3m 1l9f
Related UniProtKB P40859
[11]
Resource
Comments CHARACTERIZATION
Medline ID 20374561
PubMed ID 10913293
Journal Biochemistry
Year 2000
Volume 39
Pages 8825-9
Authors Wagner MA, Jorns MS
Title Monomeric sarcosine oxidase: 2. Kinetic studies with sarcosine, alternate substrates, and a substrate analogue.
Related PDB
Related UniProtKB P40859
[12]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10913292
Journal Biochemistry
Year 2000
Volume 39
Pages 8813-24
Authors Wagner MA, Trickey P, Chen ZW, Mathews FS, Jorns MS
Title Monomeric sarcosine oxidase: 1. Flavin reactivity and active site binding determinants.
Related PDB 1el5 1el7 1el8 1el9 1eli
Related UniProtKB
[13]
Resource
Comments CHARACTERIZATION
Medline ID 20541388
PubMed ID 11087383
Journal Biochemistry
Year 2000
Volume 39
Pages 14341-7
Authors Zhao G, Qu J, Davis FA, Jorns MS
Title Inactivation of monomeric sarcosine oxidase by reaction with N-(cyclopropyl)glycine.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11035956
Journal Protein Expr Purif
Year 2000
Volume 20
Pages 95-7
Authors Nishiya Y
Title A mutant sarcosine oxidase in which activity depends on flavin adenine dinucleotide.
Related PDB
Related UniProtKB
[15]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 12146941
Journal Biochemistry
Year 2002
Volume 41
Pages 9751-64
Authors Zhao G, Song H, Chen ZW, Mathews FS, Jorns MS
Title Monomeric sarcosine oxidase: role of histidine 269 in catalysis.
Related PDB 1l9c 1l9d 1l9e
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 12084049
Journal Eur J Biochem
Year 2002
Volume 269
Pages 3096-102
Authors Sutcliffe MJ, Scrutton NS
Title A new conceptual framework for enzyme catalysis. Hydrogen tunnelling coupled to enzyme dynamics in flavoprotein and quinoprotein enzymes.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 12549903
Journal Biochemistry
Year 2003
Volume 42
Pages 864-9
Authors Khanna P, Jorns MS
Title Tautomeric rearrangement of a dihydroflavin bound to monomeric sarcosine oxidase or N-methyltryptophan oxidase.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 15240125
Journal Biochem Biophys Res Commun
Year 2004
Volume 320
Pages 846-51
Authors Mukouyama EB, Oguchi M, Kodera Y, Maeda T, Suzuki H
Title Low pKa lysine residues at the active site of sarcosine oxidase from Corynebacterium sp. U-96.
Related PDB
Related UniProtKB

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).

Created Updated
2004-03-24 2009-02-26