2PLJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M704066200
  • Primary Citation of Related Structures:  

  • 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 polyamin ...

    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 Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
lysine/ornithine decarboxylase
A, B
419Vibrio vulnificus (strain CMCP6)Mutation(s): 0 
EC: 4.1.1.17
Find proteins for A0A3Q0KZG4 (Vibrio vulnificus (strain CMCP6))
Go to UniProtKB:  A0A3Q0KZG4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P3T
Query on P3T

Download SDF File 
Download CCD File 
A, B
(4-{[(4-AMINOBUTYL)AMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
PHOSPHORIC ACID MONO-{4-[(4-AMINO-BUTYLAMINO)-METHYL]-5-HYDROXY-6-METHYL-PYRIDIN-3-YLMETHYL} ESTER
C12 H22 N3 O5 P
MXDZELCJRJAUEI-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.074α = 90.00
b = 88.683β = 90.00
c = 111.843γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling
HKL-3000data collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2007-10-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance