2ZY5

R487A mutant of L-aspartate beta-decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1016/j.str.2009.02.013
  • Structures With Same Primary Citation

  • 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 s ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-aspartate beta-decarboxylaseA, B, C, D, E, F546Alcaligenes faecalis subsp. faecalisMutation(s): 1 
Gene Names: asdA-AF
EC: 4.1.1.12 (PDB Primary Data), 2.6.1.1 (UniProt)
Find proteins for Q93QX0 (Comamonas testosteroni)
Explore Q93QX0 
Go to UniProtKB:  Q93QX0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A, B, C, D, E, F
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.953α = 90
b = 216.215β = 90
c = 208.582γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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