6RKF | pdb_00006rkf

Structure of human DASPO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 
    0.271 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure and kinetic properties of human d-aspartate oxidase, the enzyme-controlling d-aspartate levels in brain.

Molla, G.Chaves-Sanjuan, A.Savinelli, A.Nardini, M.Pollegioni, L.

(2020) FASEB J 34: 1182-1197

  • DOI: https://doi.org/10.1096/fj.201901703R
  • Primary Citation Related Structures: 
    6RKF

  • PubMed Abstract: 

    d-Amino acids are the "wrong" enantiomers of amino acids as they are not used in proteins synthesis but evolved in selected functions. On this side, d-aspartate (d-Asp) plays several significant roles in mammals, especially as an agonist of N-methyl-d-aspartate receptors (NMDAR), and is involved in relevant diseases, such as schizophrenia and Alzheimer's disease. In vivo modulation of d-Asp levels represents an intriguing task to cope with such pathological states. As little is known about d-Asp synthesis, the only option for modulating the levels is via degradation, which is due to the flavoenzyme d-aspartate oxidase (DASPO). Here we present the first three-dimensional structure of a DASPO enzyme (from human) which belongs to the d-amino acid oxidase family. Notably, human DASPO differs from human d-amino acid oxidase (attributed to d-serine degradation, the main coagonist of NMDAR) showing peculiar structural features (a specific active site charge distribution), oligomeric state and kinetic mechanism, and a higher FAD affinity and activity. These results provide useful insights into the structure-function relationships of human DASPO: modulating its activity represents now a feasible novel therapeutic target.


  • Organizational Affiliation
    • Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, Varese, Italy.

Macromolecule Content 

  • Total Structure Weight: 238.11 kDa 
  • Atom Count: 16,135 
  • Modeled Residue Count: 2,003 
  • Deposited Residue Count: 2,100 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D-aspartate oxidase
A, B, C, D, E
A, B, C, D, E, F
350Homo sapiensMutation(s): 2 
Gene Names: DDO
EC: 1.4.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99489 (Homo sapiens)
Explore Q99489 
Go to UniProtKB:  Q99489
PHAROS:  Q99489
GTEx:  ENSG00000203797 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99489
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
G [auth A]
K [auth B]
M [auth C]
P [auth D]
R [auth E]
G [auth A],
K [auth B],
M [auth C],
P [auth D],
R [auth E],
T [auth F]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
I [auth A],
N [auth C],
U [auth F]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4

Query on PO4



Download:Ideal Coordinates CCD File
J [auth A],
W [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A]
L [auth B]
O [auth C]
Q [auth D]
S [auth E]
H [auth A],
L [auth B],
O [auth C],
Q [auth D],
S [auth E],
V [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free:  0.271 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.397α = 90
b = 159.715β = 90
c = 288.575γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description