1JS3

Crystal structure of dopa decarboxylase in complex with the inhibitor carbidopa

• PDB DOI: https://doi.org/10.2210/pdb1JS3/pdb

• Classification: LYASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-08-16 Released: 2001-10-26 
• Deposition Author(s): Burkhard, P., Dominici, P., Borri-Voltattorni, C., Jansonius, J.N., Malashkevich, V.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.187 
• R-Value Work: 0.144 
• R-Value Observed: 0.144 

Literature

Structural insight into Parkinson's disease treatment from drug-inhibited DOPA decarboxylase.

Burkhard, P., Dominici, P., Borri-Voltattorni, C., Jansonius, J.N., Malashkevich, V.N.

(2001) Nat Struct Biol 8: 963-967

• PubMed: 11685243 
• DOI: https://doi.org/10.1038/nsb1101-963
• Primary Citation of Related Structures:  
  1JS3, 1JS6


• PubMed Abstract: 
  

  DOPA decarboxylase (DDC) is responsible for the synthesis of the key neurotransmitters dopamine and serotonin via decarboxylation of L-3,4-dihydroxyphenylalanine (L-DOPA) and L-5-hydroxytryptophan, respectively. DDC has been implicated in a number of clinic disorders, including Parkinson's disease and hypertension. Peripheral inhibitors of DDC are currently used to treat these diseases. We present the crystal structures of ligand-free DDC and its complex with the anti-Parkinson drug carbiDOPA. The inhibitor is bound to the enzyme by forming a hydrazone linkage with the cofactor, and its catechol ring is deeply buried in the active site cleft. The structures provide the molecular basis for the development of new inhibitors of DDC with better pharmacological characteristics.

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Organizational Affiliation: 

M.E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 109.34 kDa 
• Atom Count: 7,787 
• Modelled Residue Count: 928 
• Deposited Residue Count: 972 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DOPA decarboxylase	A, B	486	Sus scrofa	Mutation(s): 0  EC: 4.1.1.28
UniProt
Find proteins for P80041 (Sus scrofa) Explore P80041  Go to UniProtKB:  P80041

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], I [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
142	F [auth A], J [auth B]	CARBIDOPA C10 H14 N2 O4 TZFNLOMSOLWIDK-JTQLQIEISA-N
SO4	C [auth A], D [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.187 
• R-Value Work: 0.144 
• R-Value Observed: 0.144 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.36	α = 90
b = 154.36	β = 90
c = 86.78	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	model building
CNS	refinement
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-26 
Deposition Author(s): Burkhard, P., Dominici, P., Borri-Voltattorni, C., Jansonius, J.N., Malashkevich, V.N.

Revision History  

• Version 1.0: 2001-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Structure summary