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PROSITE documentation PDOC51677 [for PROSITE entry PS51677]

NodB homology domain profile





Description

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)


References

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
DOI10.1016/j.febslet.2004.06.013

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
DOI10.1128/JB.00838-08

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
DOI10.1371/journal.pone.0019207

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
DOI10.1074/jbc.M801195200

E1Sourcehttp://www.cazy.org/CE4.html



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