dodecameric L-aspartate beta-decarboxylase

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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This is version 1.3 of the entry. See complete history


Structure, Assembly, and Mechanism of a PLP-Dependent Dodecameric l-Aspartate beta-Decarboxylase

Chen, H.-J.Ko, T.-P.Lee, C.-Y.Wang, N.-C.Wang, A.H.-J.

(2009) Structure 17: 517-529

  • DOI: https://doi.org/10.1016/j.str.2009.02.013
  • Primary Citation of Related Structures:  
    2ZY2, 2ZY3, 2ZY4, 2ZY5

  • PubMed Abstract: 

    The type-I PLP enzyme l-aspartate beta-decarboxylase converts aspartate to alanine and CO(2). Similar to the homodimeric aminotransferases, its protein subunit comprises a large and a small domain, of 410 and 120 residues, respectively. The crystal structure reveals a dodecamer made of six identical dimers arranged in a truncated tetrahedron whose assembly involves tetramer and hexamer as intermediates. The additional helical motifs I and II participate in the oligomer formation. Triple mutations of S67R/Y68R/M69R or S67E/Y68E/M69E in motif I produced an inactive dimer. The PLP is bound covalently to Lys315 in the active site, while its phosphate group interacts with a neighboring Tyr134. Removal of the bulky side chain of Arg37, which overhangs the PLP group, improved the substrate affinity. Mutations in flexible regions produced the more active K17A and the completely inactive R487A. The structure also suggests that substrate binding triggers conformational changes essential for catalyzing the reaction.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-aspartate beta-decarboxylase
A, B, C, D, E
A, B, C, D, E, F
546Alcaligenes faecalis subsp. faecalisMutation(s): 0 
Gene Names: asdA-AF
Find proteins for Q93QX0 (Comamonas testosteroni)
Explore Q93QX0 
Go to UniProtKB:  Q93QX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93QX0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
C8 H10 N O6 P
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.953α = 90
b = 217.149β = 90
c = 207.154γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description