1JS6

Crystal Structure of DOPA decarboxylase

PDB DOI: https://doi.org/10.2210/pdb1JS6/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.258
R-Value Work: 0.206
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

M.E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Peter.Burkhard@unibas.ch

Macromolecule Content

Total Structure Weight: 108.5 kDa
Atom Count: 7,375
Modelled Residue Count: 928
Deposited Residue Count: 972
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80041
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.258
R-Value Work: 0.206
R-Value Observed: 0.206
Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.86	α = 90
b = 152.86	β = 90
c = 86.6	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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 (Full details and data files)

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