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117  structures 7239  species 0  interactions 33959  sequences 548  architectures

Family: Polysacc_deac_1 (PF01522)

Summary: Polysaccharide deacetylase

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Polysaccharide deacetylase Provide feedback

This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase [1]. It also includes chitin deacetylase from yeast [2] and endoxylanases which hydrolyses glucosidic bonds in xylan [3].

Literature references

  1. Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X; , Nature 1997;387:394-401.: Molecular basis of symbiosis between Rhizobium and legumes. PUBMED:9163424 EPMC:9163424

  2. C. Mishra, C. E. Semino, K. J. McCreath, H. de la Vega, B. J. Jones, C. A. Specht & P. W. Robbins; , Yeast 1996;13:327-336.: Cloning and expression of two chitin deacetylase genes of Saccharomyces cerevisiae. PUBMED:9133736 EPMC:9133736

  3. S. J. Millward-Sadler, D. M. Poole, B. Henrissat, G. P. Hazlewood, J. H. Clarke & H. J. Gilbert; , Mol Microbiol 1994;11:375-382.: Evidence for a general role for high-affinity non-catalytic cellulose binding domains in microbial plant cell wall hydrolases. PUBMED:8170399 EPMC:8170399

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002509

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 [ PUBMED:12644381 , PUBMED:15251431 , PUBMED:18978064 , PUBMED: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 [ PUBMED: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 [ PUBMED:15251431 , PUBMED:18978064 , PUBMED:21559431 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan GH_CE (CL0158), which has the following description:

This superfamily contains diverse enzymes that act on carbohydrates including both hydrolases and deacetylases.

The clan contains the following 11 members:

DUF2194 DUF2334 DUF3863 Glyco_hydro_38N Glyco_hydro_57 GxGYxYP_C LamB_YcsF Polysacc_deac_1 Polysacc_deac_2 Polysacc_deac_3 YdjC


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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_502 (release 4.0)
Previous IDs: Polysac_deacet;Polysacc_deacet;
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 72
Number in full: 33959
Average length of the domain: 131.10 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 37.19 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.1 23.1
Trusted cut-off 23.1 23.1
Noise cut-off 23.0 23.0
Model length: 124
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Polysacc_deac_1 domain has been found. There are 117 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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