Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus

Experimental Data Snapshot

  • Resolution: 2.14 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

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Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases.

Lee, J.Michael, A.J.Martynowski, D.Goldsmith, E.J.Phillips, M.A.

(2007) J Biol Chem 282: 27115-27125

  • DOI: https://doi.org/10.1074/jbc.M704066200
  • Primary Citation of Related Structures:  
    2PLJ, 2PLK

  • PubMed Abstract: 

    The beta/alpha-barrel fold type basic amino acid decarboxylases include eukaryotic ornithine decarboxylases (ODC) and bacterial and plant enzymes with activity on L-arginine and meso-diaminopimelate. These enzymes catalyze essential steps in polyamine and lysine biosynthesis. Phylogenetic analysis suggests that diverse bacterial species also contain ODC-like enzymes from this fold type. However, in comparison with the eukaryotic ODCs, amino acid differences were identified in the sequence of the 3(10)-helix that forms a key specificity element in the active site, suggesting they might function on novel substrates. Putative decarboxylases from a phylogenetically diverse range of bacteria were characterized to determine their substrate preference. Enzymes from species within Methanosarcina, Pseudomonas, Bartonella, Nitrosomonas, Thermotoga, and Aquifex showed a strong preference for L-ornithine, whereas the enzyme from Vibrio vulnificus (VvL/ODC) had dual specificity functioning well on both L-ornithine and L-lysine. The x-ray structure of VvL/ODC was solved in the presence of the reaction products putrescine and cadaverine to 1.7 and 2.15A, respectively. The overall structure is similar to eukaryotic ODC; however, reorientation of the 3(10)-helix enlarging the substrate binding pocket allows L-lysine to be accommodated. The structure of the putrescine-bound enzyme suggests that a bridging water molecule between the shorter L-ornithine and key active site residues provides the structural basis for VvL/ODC to also function on this substrate. Our data demonstrate that there is greater structural and functional diversity in bacterial polyamine biosynthetic decarboxylases than previously suspected.

  • Organizational Affiliation

    Departments of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041 and the.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
lysine/ornithine decarboxylase
A, B
419Vibrio vulnificus CMCP6Mutation(s): 0 
Gene Names: LysA
EC: (PDB Primary Data), (PDB Primary Data)
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on P3D

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C13 H22 N3 O5 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.14 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.245α = 90
b = 88.027β = 90
c = 99.272γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata 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: 2007-07-10
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description