Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases.
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.
Department of Biochemistry and Molecular Biology and Mathematics, University of Parma, 43100, Parma, Italy.
Ileana
I
Ramazzina
Laura
L
Cendron
Claudia
C
Folli
Rodolfo
R
Berni
Daniela
D
Monteverdi
Giuseppe
G
Zanotti
Riccardo
R
Percudani
D000581:Amidohydrolases / Q000737:chemistry* / Q000378:metabolism*; D000595:Amino Acid Sequence; D001665:Binding Sites; D002384:Catalysis; D002686:Chitin / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D018360:Crystallography, X-Ray; D008969:Molecular Sequence Data; D010457:Peptidoglycan / Q000737:chemistry; D010802:Phylogeny; D011134:Polysaccharides / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D011551:Pseudomonas fluorescens / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
D010457:Peptidoglycan; D011134:Polysaccharides; D002686:Chitin; D000581:Amidohydrolases; C022427:polysaccharide deacetylase; C019659:allantoinase