Crystal structure of Puue Allantoinase

Experimental Data Snapshot

  • Resolution: 1.58 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

Starting Model: experimental
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Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases

Ramazzina, I.Cendron, L.Folli, C.Berni, R.Monteverdi, D.Zanotti, G.Percudani, R.

(2008) J Biol Chem 283: 23295-23304

  • DOI: https://doi.org/10.1074/jbc.M801195200
  • Primary Citation of Related Structures:  
    3CL6, 3CL7, 3CL8

  • PubMed Abstract: 

    The hydrolytic cleavage of the hydantoin ring of allantoin, catalyzed by allantoinase, is required for the utilization of the nitrogen present in purine-derived compounds. The allantoinase gene (DAL1), however, is missing in many completely sequenced organisms able to use allantoin as a nitrogen source. Here we show that an alternative allantoinase gene (puuE) can be precisely identified by analyzing its logic relationship with three other genes of the pathway. The novel allantoinase is annotated in structure and sequence data bases as polysaccharide deacetylase for its homology with enzymes that catalyze hydrolytic reactions on chitin or peptidoglycan substrates. The recombinant PuuE protein from Pseudomonas fluorescens exhibits metal-independent allantoinase activity and stereospecificity for the S enantiomer of allantoin. The crystal structures of the protein and of protein-inhibitor complexes reveal an overall similarity with the polysaccharide deacetylase beta/alpha barrel and remarkable differences in oligomeric assembly and active site geometry. The conserved Asp-His-His metal-binding triad is replaced by Glu-His-Trp, a configuration that is distinctive of PuuE proteins within the protein family. An extra domain at the top of the barrel offers a scaffold for protein tetramerization and forms a small substrate-binding cleft by hiding the large binding groove of polysaccharide deacetylases. Substrate positioning at the active site suggests an acid/base mechanism of catalysis in which only one member of the catalytic pair of polysaccharide deacetylases has been conserved. These data provide a structural rationale for the shifting of substrate specificity that occurred during evolution.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology and Mathematics, University of Parma, 43100, Parma, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Puue allantoinase
A, B
308Pseudomonas fluorescensMutation(s): 0 
Find proteins for Q3KFK7 (Pseudomonas fluorescens (strain Pf0-1))
Explore Q3KFK7 
Go to UniProtKB:  Q3KFK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3KFK7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.58 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.299α = 90
b = 98.299β = 90
c = 62.393γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description