3O7J

Crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Mechanistic Studies on Klebsiella pneumoniae 2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline Decarboxylase.

French, J.B.Ealick, S.E.

(2010) J.Biol.Chem. 285: 35446-35454

  • DOI: 10.1074/jbc.M110.156034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The stereospecific oxidative degradation of uric acid to (S)-allantoin was recently shown to proceed via three enzymatic steps. The final conversion is a decarboxylation of the unstable intermediate 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU ...

    The stereospecific oxidative degradation of uric acid to (S)-allantoin was recently shown to proceed via three enzymatic steps. The final conversion is a decarboxylation of the unstable intermediate 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) and is catalyzed by OHCU decarboxylase. Here we present the structures of Klebsiella pneumoniae OHCU decarboxylase in unliganded form and with bound allantoin. These structures provide evidence that ligand binding organizes the active site residues for catalysis. Modeling of the substrate and intermediates provides additional support for this hypothesis. In addition we characterize the steady state kinetics of this enzyme and report the first OHCU decarboxylase inhibitor, allopurinol, a structural isomer of hypoxanthine. This molecule is a competitive inhibitor of K. pneumoniae OHCU decarboxylase with a K(i) of 30 ± 2 μM. Circular dichroism measurements confirm structural observations that this inhibitor disrupts the necessary organization of the active site. Our structural and biochemical studies also provide further insights into the mechanism of catalysis of OHCU decarboxylation.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OHCU decarboxylase
A
189Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)Mutation(s): 0 
Find proteins for A6T925 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Go to UniProtKB:  A6T925
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2AL
Query on 2AL

Download SDF File 
Download CCD File 
A
1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA
ALLANTOIN
C4 H4 N4 O3
MFAONEQLPARJAO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.182α = 90.00
b = 47.317β = 123.13
c = 50.208γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance