Human holo aromatic L-amino acid decarboxylase (AADC) external aldimine with L-Dopa methylester

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


Human aromatic amino acid decarboxylase is an asymmetric and flexible enzyme: Implication in aromatic amino acid decarboxylase deficiency.

Bisello, G.Ribeiro, R.P.Perduca, M.Belviso, B.D.Polverino De' Laureto, P.Giorgetti, A.Caliandro, R.Bertoldi, M.

(2023) Protein Sci 32: e4732-e4732

  • DOI: https://doi.org/10.1002/pro.4732
  • Primary Citation of Related Structures:  
    8OR9, 8ORA

  • PubMed Abstract: 

    Human aromatic amino acid decarboxylase (AADC) is a pyridoxal 5'-phosphate-dependent enzyme responsible for the biosynthesis of dopamine and serotonin, essential neurotransmitters involved in motor and cognitive abilities. Mutations in its gene lead to AADC deficiency, a monogenic rare neurometabolic childhood parkinsonism characterized by severe motor and neurodevelopmental symptoms. Here, for the first time, we solved the crystal structure of human holoAADC in the internal aldimine (1.9 Å) and in the external aldimine (2.4 Å) of the substrate analog L-Dopa methylester. In this intermediate, the highly flexible AADC catalytic loop (CL) is captured in a closed state contacting all protein domains. In addition, each active site, composed by residues of both subunits, is connected to the other through weak interactions and a central cavity. By combining crystallographic analyses with all-atom and coarse-grained molecular dynamics simulations, SAXS investigations and limited proteolysis experiments, we realized that the functionally obligate homodimeric AADC enzyme in solution is an elongated, asymmetric molecule, where the fluctuations of the CL are coupled to flexibility at the edge between the N-terminal and C-terminal domains. The structural integrity of this peripheral protein region is essential to catalysis, as assessed by both artificial and 37 AADC deficiency pathogenic variants leading to the interpretation that structural dynamics in protein regions far from the active site is essential for CL flexibility and the acquirement of a correct catalytically competent structure. This could represent the molecular basis for pathogenicity prediction in AADC deficiency.

  • Organizational Affiliation

    Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, Verona, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dopa decarboxylase (Aromatic L-amino acid decarboxylase)480Homo sapiensMutation(s): 0 
Gene Names: DDChCG_1811384tcag7.584
UniProt & NIH Common Fund Data Resources
Find proteins for P20711 (Homo sapiens)
Explore P20711 
Go to UniProtKB:  P20711
PHAROS:  P20711
GTEx:  ENSG00000132437 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20711
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.642α = 90
b = 107.642β = 90
c = 218.242γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateItalyIIS PTCIT100263

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release