Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.49 kDa 
• Atom Count: 3481 
• Modelled Residue Count: 363 
• Deposited Residue Count: 363 
• Unique protein chains: 1

1C0K

CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE

• PDB DOI: 10.2210/pdb1C0K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodotorula toruloides
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-07-16 Released: 2000-11-22 
• Deposition Author(s): Umhau, S., Molla, G., Diederichs, K., Pilone, M.S., Ghisla, S., Welte, W., Pollegioni, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å

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

• PubMed: 11070076 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (D-AMINO ACID OXIDASE)	A	363	Rhodotorula toruloides	Mutation(s): 0  Gene Names: DAO1 EC: 1.4.3.3
UniProt
Find proteins for P80324 (Rhodosporidium toruloides) Explore P80324  Go to UniProtKB:  P80324

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
LAC	C [auth A]	LACTIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.67	α = 90
b = 120.67	β = 90
c = 136.37	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
SHELXL-97	refinement
MAR345	data collection
XDS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-07-16 
• Released Date: 2000-11-22 
Deposition Author(s): Umhau, S., Molla, G., Diederichs, K., Pilone, M.S., Ghisla, S., Welte, W., Pollegioni, L.

Revision History  

• 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: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description