PDBsum entry 1b3m

Oxidoreductase

PDB id: 1b3m

Contents

Protein chains

385 a.a.

Ligands

FAD ×2

Waters ×206

Obsolete entry

PDB id:

1b3m

Name:

Oxidoreductase

Title:

Monomeric sarcosine oxidase from bacillus sp. B-0618

Structure:

Protein (monomeric sarcosine oxidase). Chain: a, b. Engineered: yes

Source:

Bacillus sp.. Strain: b-0618. Expressed in: escherichia coli.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.177 R-free: 0.241

Authors:

P.Trickey,M.A.Wagner,M.S.Jorns,F.S.Mathews

Key ref:

P.Trickey et al. (1999). Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme. Structure Fold Des, 7, 331-345. PubMed id: 10368302 DOI: 10.1016/S0969-2126(99)80043-4

Date:

12-Dec-98 Release date: 18-Feb-00

Protein chains

P40859  (SAOX_BACSP) -  Monomeric sarcosine oxidase from Bacillus sp. (strain B-0618)

Seq: 390 a.a.

Struc: 385 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.5.3.1 - sarcosine oxidasee (formaldehyde-forming).
• Reaction: sarcosine + O2 + H2O = formaldehyde + glycine + H2O2
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) matches with 41.33% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0969-2126(99)80043-4

Structure Fold Des 7:331-345 (1999)

PubMed id: 10368302

Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.

P.Trickey, M.A.Wagner, M.S.Jorns, F.S.Mathews.

ABSTRACT

BACKGROUND: Monomeric sarcosine oxidases (MSOXs) are among the simplest members of a recently recognized family of eukaryotic and prokaryotic enzymes that catalyze similar oxidative reactions with various secondary or tertiary amino acids and contain covalently bound flavins. Other members of this family include heterotetrameric sarcosine oxidase, N-methyltryptophan oxidase and pipecolate oxidase. Mammalian sarcosine dehydrogenase and dimethylglycine dehydrogenase may be more distantly related family members. RESULTS: The X-ray crystal structure of MSOX from Bacillus sp. B-0618, expressed in Escherichia coli, has been solved at 2.0 A resolution by multiwavelength anomalous dispersion (MAD) from crystals of the selenomethionine-substituted enzyme. Fourteen selenium sites, belonging to two MSOX molecules in the asymmetric unit, were used for MAD phasing and to define the local twofold symmetry axis for electron-density averaging. The structures of the native enzyme and of two enzyme-inhibitor complexes were also determined. CONCLUSIONS: MSOX is a two-domain protein with an overall topology most similar to that of D-amino acid oxidase, with which it shares 14% sequence identity. The flavin ring is located in a very basic environment, making contact with sidechains of arginine, lysine, histidine and the N-terminal end of a helix dipole. The flavin is covalently attached through an 8alpha-S-cysteinyl linkage to Cys315 of the catalytic domain. Covalent attachment is probably self-catalyzed through interactions with the positive sidechains and the helix dipole. Substrate binding is probably stabilized by hydrogen bonds between the substrate carboxylate and two basic sidechains, Arg52 and Lys348, located above the re face of the flavin ring.

Selected figure(s)

Figure 7.
Figure 7. Proposed mechanism for covalent flavinylation in MSOX (Scheme III).

The above figure is reprinted by permission from Cell Press: Structure Fold Des (1999, 7, 331-345) copyright 1999.

Figure was selected by an automated process.