1C0P

D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.150 
  • R-Value Observed: 0.116 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.

Umhau, S.Pollegioni, L.Molla, G.Diederichs, K.Welte, W.Pilone, M.S.Ghisla, S.

(2000) Proc Natl Acad Sci U S A 97: 12463-12468

  • DOI: 10.1073/pnas.97.23.12463
  • Primary Citation of Related Structures:  
    1C0K, 1C0L, 1C0P

  • PubMed Abstract: 
  • Flavin is one of the most versatile redox cofactors in nature and is used by many enzymes to perform a multitude of chemical reactions. d-Amino acid oxidase (DAAO), a member of the flavoprotein oxidase family, is regarded as a key enzyme for the understanding of the mechanism underlying flavin catalysis ...

    Flavin is one of the most versatile redox cofactors in nature and is used by many enzymes to perform a multitude of chemical reactions. d-Amino acid oxidase (DAAO), a member of the flavoprotein oxidase family, is regarded as a key enzyme for the understanding of the mechanism underlying flavin catalysis. The very high-resolution structures of yeast DAAO complexed with d-alanine, d-trifluoroalanine, and l-lactate (1.20, 1.47, and 1.72 A) provide strong evidence for hydride transfer as the mechanism of dehydrogenation. This is inconsistent with the alternative carbanion mechanism originally favored for this type of enzymatic reaction. The step of hydride transfer can proceed without involvement of amino acid functional groups. These structures, together with results from site-directed mutagenesis, point to orbital orientation/steering as the major factor in catalysis. A diatomic species, proposed to be a peroxide, is found at the active center and on the Re-side of the flavin. These results are of general relevance for the mechanisms of flavoproteins and lead to the proposal of a common dehydrogenation mechanism for oxidases and dehydrogenases.


    Organizational Affiliation

    Section of Biology, University of Konstanz, P. O. Box 5560-M644, D-78434 Konstanz, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-AMINO ACID OXIDASEA363Rhodotorula toruloidesMutation(s): 0 
Gene Names: DAO1
EC: 1.4.3.3
UniProt
Find proteins for P80324 (Rhodosporidium toruloides)
Explore P80324 
Go to UniProtKB:  P80324
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DAL
Query on DAL

Download Ideal Coordinates CCD File 
C [auth A]D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
 Ligand Interaction
PER
Query on PER

Download Ideal Coordinates CCD File 
D [auth A]PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.150 
  • R-Value Observed: 0.116 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.885α = 90
b = 120.885β = 90
c = 136.364γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
MAR345data collection
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description