3FDD

The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of the Pseudomonas dacunhae aspartate-beta-decarboxylase dodecamer reveals an unknown oligomeric assembly for a pyridoxal-5'-phosphate-dependent enzyme.

Lima, S.Sundararaju, B.Huang, C.Khristoforov, R.Momany, C.Phillips, R.S.

(2009) J.Mol.Biol. 388: 98-108

  • DOI: 10.1016/j.jmb.2009.02.055

  • PubMed Abstract: 
  • The Pseudomonas dacunhael-aspartate-beta-decarboxylase (ABDC, aspartate 4-decarboxylase, aspartate 4-carboxylyase, E.C. 4.1.1.12) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the beta-decarboxylation of l-aspartate to produce l-a ...

    The Pseudomonas dacunhael-aspartate-beta-decarboxylase (ABDC, aspartate 4-decarboxylase, aspartate 4-carboxylyase, E.C. 4.1.1.12) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the beta-decarboxylation of l-aspartate to produce l-alanine and CO(2). This catalytically versatile enzyme is known to form functional dodecamers at its optimal pH and is thought to work in conjunction with an l-Asp/l-Ala antiporter to establish a proton gradient across the membrane that can be used for ATP biosynthesis. We have solved the atomic structure of ABDC to 2.35 A resolution using single-wavelength anomalous dispersion phasing. The structure reveals that ABDC oligomerizes as a homododecamer in an unknown mode among PLP-dependent enzymes and has highest structural homology with members of the PLP-dependent aspartate aminotransferase subfamily. The structure shows that the ABDC active site is very similar to that of aspartate aminotransferase. However, an additional arginine side chain (Arg37) was observed flanking the re-side of the PLP ring in the ABDC active site. The mutagenesis results show that although Arg37 is not required for activity, it appears to be involved in the ABDC catalytic cycle.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-aspartate-beta-decarboxylase
A
533Pseudomonas dacunhae ATCC 21192Mutation(s): 0 
Gene Names: aspD
EC: 2.6.1.-
Find proteins for Q845W8 (Pseudomonas dacunhae ATCC 21192)
Go to UniProtKB:  Q845W8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 150.453α = 90.00
b = 150.453β = 90.00
c = 150.453γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
REFMACrefinement
PHASERphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance