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72  structures 4046  species 1  interaction 15757  sequences 300  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_38 Glyco_hydro_57 GxGYxYP_C LamB_YcsF Polysacc_deac_1 Polysacc_deac_2 Polysacc_deac_3 YdjC

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(80)
Full
(15757)
Representative proteomes UniProt
(45119)
NCBI
(78285)
Meta
(2949)
RP15
(3107)
RP35
(9164)
RP55
(15642)
RP75
(24357)
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PP/heatmap 1                

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(80)
Full
(15757)
Representative proteomes UniProt
(45119)
NCBI
(78285)
Meta
(2949)
RP15
(3107)
RP35
(9164)
RP55
(15642)
RP75
(24357)
Alignment:
Format:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(80)
Full
(15757)
Representative proteomes UniProt
(45119)
NCBI
(78285)
Meta
(2949)
RP15
(3107)
RP35
(9164)
RP55
(15642)
RP75
(24357)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

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.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_502 (release 4.0)
Previous IDs: Polysac_deacet;Polysacc_deacet;
Type: Family
Author: Bashton M, Bateman A
Number in seed: 80
Number in full: 15757
Average length of the domain: 131.10 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 37.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -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: 20
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Polysacc_deac_1

Structures

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 72 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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