1DDO

REDUCED D-AMINO ACID OXIDASE FROM PIG KIDNEY IN COMPLEX WITH IMINO-TRP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

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

(1997) Biochemistry 36: 5853-5860

  • DOI: 10.1021/bi9630570
  • Primary Citation of Related Structures:  
    1DAO, 1DDO

  • PubMed 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) ...

    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.


    Organizational Affiliation

    Dipartimento di Genetica e Microbiologia, Universita di Pavia, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-AMINO ACID OXIDASEA, B, C, D, E, F, G, H347Sus scrofaMutation(s): 0 
Gene Names: DAO
EC: 1.4.3.3
UniProt
Find proteins for P00371 (Sus scrofa)
Explore P00371 
Go to UniProtKB:  P00371
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], T [auth F], W [auth G], Y [auth H]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
DTR (Subject of Investigation/LOI)
Query on DTR

Download Ideal Coordinates CCD File 
S [auth E], V [auth F]D-TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-SECBINFHSA-N
 Ligand Interaction
ITR (Subject of Investigation/LOI)
Query on ITR

Download Ideal Coordinates CCD File 
J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], U [auth F], X [auth G], Z [auth H]IMINO-TRYPTOPHAN
C11 H10 N2 O2
LKYWXXAVLLVJAS-XFXZXTDPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 325.2α = 90
b = 137.1β = 90
c = 196.8γ = 90
Software Package:
Software NamePurpose
DMmodel building
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-07-23
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance