1C0I

CRYSTAL STRUCTURE OF D-AMINO ACID OXIDASE IN COMPLEX WITH TWO ANTHRANYLATE MOLECULES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Yeast d-amino Acid oxidase: structural basis of its catalytic properties

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

(2002) J Mol Biol 324: 535-546

  • DOI: 10.1016/s0022-2836(02)01062-8
  • Primary Citation of Related Structures:  
    1C0I

  • PubMed Abstract: 
  • The 3D structure of the flavoprotein D-amino acid oxidase (DAAO) from the yeast Rhodotorula gracilis (RgDAAO) in complex with the competitive inhibitor anthranilate was solved (resolution 1.9A) and structural features relevant for the overall conformation and for catalytic activity are described ...

    The 3D structure of the flavoprotein D-amino acid oxidase (DAAO) from the yeast Rhodotorula gracilis (RgDAAO) in complex with the competitive inhibitor anthranilate was solved (resolution 1.9A) and structural features relevant for the overall conformation and for catalytic activity are described. The FAD is bound in an elongated conformation in the core of the enzyme. Two anthranilate molecules are found within the active site cavity; one is located in a funnel forming the entrance, and the second is in contact with the flavin. The anchoring of the ligand carboxylate with Arg285 and Tyr223 is found for all complexes studied. However, while the active site group Tyr238-OH interacts with the carboxylate in the case of the substrate D-alanine, of D-CF(3)-alanine, or of L-lactate, in the anthranilate complex the phenol group rotates around the C2-C3 bond thus opening the entrance of the active site, and interacts there with the second bound anthranilate. This movement serves in channeling substrate to the bottom of the active site, the locus of chemical catalysis. The absence in RgDAAO of the "lid" covering the active site, as found in mammalian DAAO, is interpreted as being at the origin of the differences in kinetic mechanism between the two enzymes. This lid has been proposed to regulate product dissociation in the latter, while the side-chain of Tyr238 might exert a similar role in RgDAAO. The more open active site architecture of RgDAAO is the origin of its much broader substrate specificity. The RgDAAO enzyme forms a homodimer with C2 symmetry that is different from that reported for mammalian D-amino acid oxidase. This different mode of aggregation probably causes the differences in stability and tightness of FAD cofactor binding between the DAAOs from different sources.


    Organizational Affiliation

    Department of Structural and Functional Biology, University of Insubria via J.H. Dunant, 3, 21100, Varese, Italy.



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 2 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
BE2
Query on BE2

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]2-AMINOBENZOIC ACID
C7 H7 N O2
RWZYAGGXGHYGMB-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BE2 Binding MOAD:  1C0I Kd: 2.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.83α = 90
b = 120.83β = 90
c = 136.806γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
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: 2002-02-27
    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
  • Version 1.4: 2018-02-07
    Changes: Experimental preparation
  • Version 1.5: 2018-04-04
    Changes: Data collection
  • Version 1.6: 2019-07-24
    Changes: Data collection, Refinement description