PROSITE documentation PDOC51677
NodB homology domain profile


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) [E1] 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 [1,2,3,4].

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 [5].

The NodB homology domain adopts a deformed (β/α) barrel fold comprising eight parallel β-strands, with the C-terminal ends of five of these strands forming the solvent-exposed active site region, surrounded by eight α-helices (see <PDB:2W3Z>) [2,3,4].

The profile we developed covers the entire NodB homology domain.

Last update:

June 2013 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

NODB, PS51677; NodB homology domain profile  (MATRIX)


1AuthorsCaufrier F. Martinou A. Dupont C. Bouriotis V.
TitleCarbohydrate esterase family 4 enzymes: substrate specificity.
SourceCarbohydr. Res. 338:687-692(2003).
PubMed ID12644381

2AuthorsBlair D.E. van Aalten D.M.F.
TitleStructures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine.
SourceFEBS Lett. 570:13-19(2004).
PubMed ID15251431

3AuthorsDeng D.M. Urch J.E. ten Cate J.M. Rao V.A. van Aalten D.M. Crielaard W.
TitleStreptococcus mutans SMU.623c codes for a functional, metal-dependent polysaccharide deacetylase that modulates interactions with salivary agglutinin.
SourceJ. Bacteriol. 191:394-402(2009).
PubMed ID18978064

4AuthorsShaik M.M. Cendron L. Percudani R. Zanotti G.
TitleThe structure of Helicobacter pylori HP0310 reveals an atypical peptidoglycan deacetylase.
SourcePLoS ONE 6:E19207-E19207(2011).
PubMed ID21559431

5AuthorsRamazzina I. Cendron L. Folli C. Berni R. Monteverdi D. Zanotti G. Percudani R.
TitleLogical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases.
SourceJ. Biol. Chem. 283:23295-23304(2008).
PubMed ID18550550


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