1AN9

D-AMINO ACID OXIDASE COMPLEX WITH O-AMINOBENZOATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex.

Miura, R.Setoyama, C.Nishina, Y.Shiga, K.Mizutani, H.Miyahara, I.Hirotsu, K.

(1997) J.Biochem.(Tokyo) 122: 825-833


  • PubMed Abstract: 
  • As an extension of our recent X-ray crystallographic determination of the tertiary structure of D-amino acid oxidase (DAO) [Mizutani, H. et al. (1996) J. Biochem. 120, 14-17], we solved the crystal structure of the complex of DAO with a substrate ana ...

    As an extension of our recent X-ray crystallographic determination of the tertiary structure of D-amino acid oxidase (DAO) [Mizutani, H. et al. (1996) J. Biochem. 120, 14-17], we solved the crystal structure of the complex of DAO with a substrate analog, o-aminobenzoate (OAB). The alignment between flavin and OAB in the crystal structure of the complex is consistent with charge-transfer interaction through the overlap between the highest occupied molecular orbital of OAB and the lowest unoccupied molecular orbital of flavin. Starting with the atomic coordinates of this complex as the initial model, we carried out molecular mechanics simulation for the DAO-D-leucine complex and thus obtained a model for the enzyme-substrate complex. According to the enzyme-substrate complex model, the alpha-proton is pointed toward N(5) of flavin while the lone-pair of the substrate amino group can approach C(4a) of flavin within an interacting distance. This model as well as DAO-OAB complex enables the evaluation of the substrate-flavin interaction prior to electron transfer from the substrate to flavin and provides two possible mechanisms for the reductive-half reaction of DAO, i.e., the electron-proton-electron transfer mechanism and the ionic mechanism.


    Related Citations: 
    • Three-Dimensional Structure of Porcine Kidney D-Amino Acid Oxidase at 3.0 A Resolution
      Mizutani, H.,Miyahara, I.,Hirotsu, K.,Nishina, Y.,Shiga, K.,Setoyama, C.,Miura, R.
      (1996) J.Biochem.(Tokyo) 120: 14


    Organizational Affiliation

    Department of Biochemistry, Kumamoto University School of Medicine. miura@gpo.kumamoto-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-AMINO ACID OXIDASE
A, B
340Sus scrofaGene Names: DAO
EC: 1.4.3.3
Find proteins for P00371 (Sus scrofa)
Go to Gene View: DAO
Go to UniProtKB:  P00371
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
BE2
Query on BE2

Download SDF File 
Download CCD File 
A, B
2-AMINOBENZOIC ACID
C7 H7 N O2
RWZYAGGXGHYGMB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.310α = 90.00
b = 92.580β = 90.00
c = 71.320γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance