PDBsum entry 1dao

Flavoenzyme

PDB id: 1dao

Contents

Protein chains

(+ 2 more) 339 a.a. *

Ligands

FAB ×8

Waters ×8

* Residue conservation analysis

PDB id:

1dao

Name:

Flavoenzyme

Title:

Covalent adduct of d-amino acid oxidase from pig kidney with 3-methyl- 2-oxo-valeric acid

Structure:

D-amino acid oxidase. Chain: a, b, c, d, e, f, g, h. Synonym: daao. Ec: 1.4.3.3

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organ: kidney. Organelle: peroxisome

Biol. unit:

Dimer (from PDB file)

Resolution:

3.20Å R-factor: 0.232 R-free: 0.260

Authors:

F.Todone,A.Mattevi

Key ref:

F.Todone et al. (1997). Active site plasticity in D-amino acid oxidase: a crystallographic analysis. Biochemistry, 36, 5853-5860. PubMed id: 9153426 DOI: 10.1021/bi9630570

Date:

16-Jan-97 Release date: 23-Jul-97

Protein chains

P00371  (OXDA_PIG) -  D-amino-acid oxidase from Sus scrofa

Seq: 347 a.a.

Struc: 339 a.a.

Enzyme reactions

• Enzyme class: E.C.1.4.3.3 - D-amino-acid oxidase.
• Pathway: Cephalosporin Biosynthesis
• Reaction: a D-alpha-amino acid + O2 + H2O = a 2-oxocarboxylate + H2O2 + NH4⁺
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAB) matches with 91.38% similarity)

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

reference

DOI no: 10.1021/bi9630570

Biochemistry 36:5853-5860 (1997)

PubMed id: 9153426

Active site plasticity in D-amino acid oxidase: a crystallographic analysis.

F.Todone, M.A.Vanoni, A.Mozzarelli, M.Bolognesi, A.Coda, B.Curti, A.Mattevi.

ABSTRACT

D-Amino acid oxidase (DAAO) is the prototype of the flavin-containing oxidases. It catalyzes the oxidative deamination of various D-amino acids, ranging from D-Ala to D-Trp. We have carried out the X-ray analysis of reduced DAAO in complex with the reaction product imino tryptophan (iTrp) and of the covalent adduct generated by the photoinduced reaction of the flavin with 3-methyl-2-oxobutyric acid (kVal). These structures were solved by combination of 8-fold density averaging and least-squares refinement techniques. The FAD redox state of DAAO crystals was assessed by single-crystal polarized absorption microspectrophotometry. iTrp binds to the reduced enzyme with the N, C alpha, C, and C beta atoms positioned 3.8 A from the re side of the flavin. The indole side chain points away from the cofactor and is bound in the active site through a rotation of Tyr224. This residue plays a crucial role in that it adapts its conformation to the size of the active site ligand, providing the enzyme with the plasticity required for binding a broad range of substrates. The iTrp binding mode is fully consistent with the proposal, inferred from the analysis of the native DAAO structure, that substrate oxidation occurs via direct hydride transfer from the C alpha to the flavin N5 atom. In this regard, it is remarkable that, even in the presence of the bulky iTrp ligand, the active center is made solvent inaccessible by loop 216-228. This loop is thought to switch between the "closed" conformation observed in the crystal structures and an "open" state required for substrate binding and product release. Loop closure is likely to have a role in catalysis by increasing the hydrophobicity of the active site, thus making the hydride transfer reaction more effective. Binding of kVal leads to keto acid decarboxylation and formation of a covalent bond between the keto acid C alpha and the flavin N5 atoms. Formation of this acyl adduct results in a nonplanar flavin, characterized by a 22 degrees angle between the pyrimidine and benzene rings. Thus, in addition to an adaptable substrate binding site, DAAO has the ability to bind a highly distorted cofactor. This ability is relevant for the enzyme's function as a highly efficient oxidase.