3O7J | pdb_00003o7j

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

• PDB DOI: https://doi.org/10.2210/pdb3O7J/pdb

• Classification: LYASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-30 Released: 2010-09-08 
• Deposition Author(s): French, J.B., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.213 (Depositor) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

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 Biological Chem 285: 35446-35454

• PubMed: 20826786 
• DOI: https://doi.org/10.1074/jbc.M110.156034
• Primary Citation Related Structures: 
  3O7H, 3O7I, 3O7J, 3O7K


• 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) 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.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.99 kDa 
• Atom Count: 1,370 
• Modeled Residue Count: 166 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OHCU decarboxylase	A	189	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: KPN78578_16350, KPN_01665 EC: 4.1.1.97
UniProt
Find proteins for A6T925 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T925  Go to UniProtKB:  A6T925

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2AL	B [auth A]	1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA C4 H4 N4 O3 MFAONEQLPARJAO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.213 (Depositor) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.182	α = 90
b = 47.317	β = 123.13
c = 50.208	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): French, J.B., Ealick, S.E.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description