Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40490.55 
• Atom Count: 2858 
• Residue Count: 363 
• Unique protein chains: 1

1C0K

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

• DOI: 10.2210/pdb1C0K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodosporidium toruloides
• Expression System: Escherichia coli


• 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.USA 97: 12463-12468

• PubMed: 11070076 
• DOI: 10.1073/pnas.97.23.12463
• Primary Citation of Related Structures:  
  1C0P, 1C0L


• 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

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
LAC	A	LACTIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-UWTATZPHSA-N
FAD	A	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-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 = 120.670	α = 90.00
b = 120.670	β = 90.00
c = 136.370	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-04
  Type: Refinement description