3QVL

Allantoin racemase from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization of the Structure and Function of Klebsiella pneumoniae Allantoin Racemase.

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

(2011) J Mol Biol 410: 447-460

  • DOI: 10.1016/j.jmb.2011.05.016
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The oxidative catabolism of uric acid produces 5-hydroxyisourate (HIU), which is further degraded to (S)-allantoin by two enzymes, HIU hydrolase and 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase. The intermediates of the latter two reac ...

    The oxidative catabolism of uric acid produces 5-hydroxyisourate (HIU), which is further degraded to (S)-allantoin by two enzymes, HIU hydrolase and 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase. The intermediates of the latter two reactions, HIU and 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, are unstable in solution and decay nonstereospecifically to allantoin. In addition, nonenzymatic racemization of allantoin has been shown to occur at physiological pH. Since the further breakdown of allantoin is catalyzed by allantoinase, an enzyme that is specific for (S)-allantoin, an allantoin racemase is necessary for complete and efficient catabolism of uric acid. In this work, we characterize the structure and activity of allantoin racemase from Klebsiella pneumoniae (KpHpxA). In addition to an unliganded structure solved using selenomethionyl single-wavelength anomalous dispersion, structures of C79S/C184S KpHpxA in complex with allantoin and with 5-acetylhydantoin are presented. These structures reveal several important features of the active site including an oxyanion hole and a polar binding pocket that interacts with the ureido tail of allantoin and serves to control the orientation of the hydantoin ring. The ability of KpHpxA to interconvert the (R)- and (S)-enantiomers of allantoin is demonstrated, and analysis of the steady-state kinetics of KpHpxA yielded a k(cat)/K(m) of 6.0 × 10(5) M(-1) s(-1). Mutation of either of the active-site cysteines, Cys79 or Cys184, to serine inactivates this enzyme. The data presented provide new insights into the activity and substrate specificity of this enzyme and enable us to propose a mechanism for catalysis that is consistent with the two-base mechanism observed in other members of the aspartate/glutamate family.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative hydantoin racemaseA, B245Klebsiella pneumoniae subsp. pneumoniae MGH 78578Mutation(s): 0 
Gene Names: HpxAKPN78578_17580KPN_01788
Find proteins for A6T9E8 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6T9E8 
Go to UniProtKB:  A6T9E8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5HY
Query on 5HY

Download CCD File 
A, B
[(4R)-2,5-dioxoimidazolidin-4-yl]acetic acid
C5 H6 N2 O4
DQQLZADYSWBCOX-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.955α = 90
b = 124.955β = 90
c = 126.954γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description