PROSITE documentation PDOC51677NodB 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.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Caufrier F. Martinou A. Dupont C. Bouriotis V. |
| Title | Carbohydrate esterase family 4 enzymes: substrate specificity. | |
| Source | Carbohydr. Res. 338:687-692(2003). | |
| PubMed ID | 12644381 |
| 2 | Authors | Blair D.E. van Aalten D.M.F. |
| Title | Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine. | |
| Source | FEBS Lett. 570:13-19(2004). | |
| PubMed ID | 15251431 | |
| DOI | 10.1016/j.febslet.2004.06.013 |
| 3 | Authors | Deng D.M. Urch J.E. ten Cate J.M. Rao V.A. van Aalten D.M. Crielaard W. |
| Title | Streptococcus mutans SMU.623c codes for a functional, metal-dependent polysaccharide deacetylase that modulates interactions with salivary agglutinin. | |
| Source | J. Bacteriol. 191:394-402(2009). | |
| PubMed ID | 18978064 | |
| DOI | 10.1128/JB.00838-08 |
| 4 | Authors | Shaik M.M. Cendron L. Percudani R. Zanotti G. |
| Title | The structure of Helicobacter pylori HP0310 reveals an atypical peptidoglycan deacetylase. | |
| Source | PLoS ONE 6:E19207-E19207(2011). | |
| PubMed ID | 21559431 | |
| DOI | 10.1371/journal.pone.0019207 |
| 5 | Authors | Ramazzina I. Cendron L. Folli C. Berni R. Monteverdi D. Zanotti G. Percudani R. |
| Title | Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases. | |
| Source | J. Biol. Chem. 283:23295-23304(2008). | |
| PubMed ID | 18550550 | |
| DOI | 10.1074/jbc.M801195200 |
| E1 | Source | http://www.cazy.org/CE4.html |
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