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 
  • R-Value Observed: 0.170 

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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
  • Primary Citation of Related Structures:  
    3FDD

  • 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-alanine and CO(2) ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-aspartate-beta-decarboxylaseA533[Pseudomonas] dacunhae ATCC 21192Mutation(s): 0 
Gene Names: aspDGI:28875527
EC: 4.1.1.12 (PDB Primary Data), 2.6.1 (UniProt)
UniProt
Find proteins for Q845W8 ([Pseudomonas] dacunhae ATCC 21192)
Explore Q845W8 
Go to UniProtKB:  Q845W8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ845W8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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 
  • R-Value Observed: 0.170 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.453α = 90
b = 150.453β = 90
c = 150.453γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data 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: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance