3K40

Crystal structure of Drosophila 3,4-dihydroxyphenylalanine decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb3K40/pdb

• Classification: LYASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-05 Released: 2010-02-02 
• Deposition Author(s): Han, Q., Ding, H., Robinson, H., Christensen, B.M., Li, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.226 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Literature

Crystal structure and substrate specificity of Drosophila 3,4-dihydroxyphenylalanine decarboxylase

Han, Q., Ding, H., Robinson, H., Christensen, B.M., Li, J.

(2010) PLoS One 5: e8826-e8826

• PubMed: 20098687 
• DOI: https://doi.org/10.1371/journal.pone.0008826
• Primary Citation of Related Structures:  
  3K40


• PubMed Abstract: 
  

  3,4-Dihydroxyphenylalanine decarboxylase (DDC), also known as aromatic L-amino acid decarboxylase, catalyzes the decarboxylation of a number of aromatic L-amino acids. Physiologically, DDC is responsible for the production of dopamine and serotonin through the decarboxylation of 3,4-dihydroxyphenylalanine and 5-hydroxytryptophan, respectively. In insects, both dopamine and serotonin serve as classical neurotransmitters, neuromodulators, or neurohormones, and dopamine is also involved in insect cuticle formation, eggshell hardening, and immune responses.

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Organizational Affiliation: 

Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America.

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: 107.83 kDa 
• Atom Count: 7,715 
• Modelled Residue Count: 896 
• Deposited Residue Count: 950 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic-L-amino-acid decarboxylase	A, B	475	Drosophila melanogaster	Mutation(s): 0  Gene Names: CG10697, Ddc EC: 4.1.1.28
UniProt
Find proteins for P05031 (Drosophila melanogaster) Explore P05031  Go to UniProtKB:  P05031

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.226 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.809	α = 90
b = 108.597	β = 90
c = 86.294	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-02 
Deposition Author(s): Han, Q., Ding, H., Robinson, H., Christensen, B.M., Li, J.

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection