InterPro domain: IPR002509

The NodB homology domain is a catalytic domain of ~200 amino acid residues,which has been named after its similarity to rhizobial NodBchitooligosaccharide deacetylase. It is found in members of carbohydrateesterase family 4 (CE4) and in PuuE proteins.

Members of the CE4 family exhibit metal-dependent deacetylation of O- and N-acetylated polysaccharides, such as chitin, peptidoglycan, and acetylxylan.Proteins belonging to this family have conserved residues that are importantfor metal coordination (D-H-H triad) and enzymatic activity. CE4 enzymestypically require a divalent Zn(2+) or Ni(2+) metal ion that is usuallycoordinated by an aspartate and two histidine residues [ 1 , 2 , 3 , 4 ].

PuuE proteins are allantoinases that catalyze the hydrolytic cleavage of thehydantoin ring of allantoin. The conserved D-H-H metal-binding triad isreplaced by E-H-W in PuuE proteins. Amino acid substitutions are also observedfor residues that have been implicated in catalysis, conferring metalindependency to the enzyme [ 5 ].

The NodB homology domain adopts a deformed (beta/alpha) barrel fold comprisingeight parallel beta-strands, with the C-terminal ends of five of these strandsforming the solvent-exposed active site region, surrounded by eight alpha-helices [ 6 , 6 , 6 ].

1. Carbohydrate esterase family 4 enzymes: substrate specificity. Carbohydr. Res. 338, 687-92
2. Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine. FEBS Lett. 570, 13-9
3. Streptococcus mutans SMU.623c codes for a functional, metal-dependent polysaccharide deacetylase that modulates interactions with salivary agglutinin. J. Bacteriol. 191, 394-402
4. The structure of Helicobacter pylori HP0310 reveals an atypical peptidoglycan deacetylase. PLoS ONE 6, e19207
5. Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases. J. Biol. Chem. 283, 23295-304