NodB homology domain (IPR002509)

Short name: NODB_dom

Overlapping homologous superfamilies

Domain relationships


The NodB homology domain is a catalytic domain of ~200 amino acid residues, which has been named after its similarity to rhizobial NodB chitooligosaccharide deacetylase. It is found in members of carbohydrate esterase 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 important for metal coordination (D-H-H triad) and enzymatic activity. CE4 enzymes typically require a divalent Zn(2+) or Ni(2+) metal ion that is usually coordinated by an aspartate and two histidine residues [PMID: 12644381, PMID: 15251431, PMID: 18978064, PMID: 21559431].

PuuE proteins are allantoinases that catalyze the hydrolytic cleavage of the hydantoin ring of allantoin. The conserved D-H-H metal-binding triad is replaced by E-H-W in PuuE proteins. Amino acid substitutions are also observed for residues that have been implicated in catalysis, conferring metal independency to the enzyme [PMID: 18550550].

The NodB homology domain adopts a deformed (beta/alpha) barrel fold comprising eight parallel beta-strands, with the C-terminal ends of five of these strands forming the solvent-exposed active site region, surrounded by eight alpha- helices [PMID: 15251431, PMID: 18978064, PMID: 21559431].

GO terms

Biological Process

GO:0005975 carbohydrate metabolic process

Molecular Function

GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE profiles