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23  structures 3331  species 0  interactions 5902  sequences 439  architectures

Family: Glucosaminidase (PF01832)

Summary: Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Glycoside hydrolase family 73". More...

Glycoside hydrolase family 73 Edit Wikipedia article

Glucosaminidase
Identifiers
SymbolGlucosaminidase
PfamPF01832
Pfam clanCL0037
InterProIPR002901
CAZyGH73

In molecular biology, glycoside hydrolase family 73 is a family of glycoside hydrolases.

Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families.[1][2][3] This classification is available on the CAZy(http://www.cazy.org/GH1.html) web site,[4] and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes. [5]

Glycoside hydrolase family 73 CAZY GH_73 includes peptidoglycan hydrolases with endo-β-N-acetylglucosaminidase specificity. Members of this family include mannosyl-glycoprotein endo-beta-N-acetylglucosamidase EC 3.2.1.96 and flagellar protein J (flgJ), which has been shown to hydrolyse peptidoglycan.[6]


References

  1. ^ Henrissat B, Callebaut I, Mornon JP, Fabrega S, Lehn P, Davies G (1995). "Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases". Proc. Natl. Acad. Sci. U.S.A. 92 (15): 7090–7094. doi:10.1073/pnas.92.15.7090. PMC 41477. PMID 7624375.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ Henrissat B, Davies G (1995). "Structures and mechanisms of glycosyl hydrolases". Structure. 3 (9): 853–859. doi:10.1016/S0969-2126(01)00220-9. PMID 8535779.
  3. ^ Bairoch, A. "Classification of glycosyl hydrolase families and index of glycosyl hydrolase entries in SWISS-PROT". 1999.
  4. ^ Henrissat, B. and Coutinho P.M. "Carbohydrate-Active Enzymes server". 1999.
  5. ^ CAZypedia, an online encyclopedia of carbohydrate-active enzymes.
  6. ^ Nambu T, Minamino T, Macnab RM, Kutsukake K (1999). "Peptidoglycan-hydrolyzing activity of the FlgJ protein, essential for flagellar rod formation in Salmonella typhimurium". J. Bacteriol. 181 (5): 1555–61. PMC 93546. PMID 10049388. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR002901

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase Provide feedback

This family includes Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase EC:3.2.1.96. As well as the flageller protein J P75942 that has been shown to hydrolyse peptidoglycan [1].

Literature references

  1. Nambu T, Minamino T, Macnab RM, Kutsukake K; , J Bacteriol 1999;181:1555-1561.: Peptidoglycan-hydrolyzing activity of the FlgJ protein, essential for flagellar rod formation in Salmonella typhimurium. PUBMED:10049388 EPMC:10049388


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002901

This domain is found in many different proteins including mannosyl-glycoprotein endo-beta-N-acetylglucosamidase ( EC ). It is also found in flagellar protein J ( SWISSPROT ), which has been shown to hydrolyse peptidoglycan [ PUBMED:10049388 ].

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 Lysozyme (CL0037), which has the following description:

Barley chitinase, bacterial chitosanase, and lysozymes from phage and animals all hydrolyse related polysaccharides. The proteins little amino-acid similarity, but have a structurally invariant core consisting of two helices and a three-stranded beta-sheet which form the substrate-binding and catalytic cleft [1].

The clan contains the following 21 members:

Destabilase DUF3218 Glucosaminidase Glyco_hydro_108 Glyco_hydro_19 Glyco_hydro_46 Glyco_hydro_80 Lys Lysozyme_like Peptidase_U40 Pesticin Phage_lysozyme Phage_lysozyme2 SLT SLT_2 SLT_3 SLT_4 TraH_2 Transgly Transglycosylas Utp11

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 and the UniProtKB 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
(539)
Full
(5902)
Representative proteomes UniProt
(33529)
RP15
(914)
RP35
(2931)
RP55
(6054)
RP75
(11015)
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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
(539)
Full
(5902)
Representative proteomes UniProt
(33529)
RP15
(914)
RP35
(2931)
RP55
(6054)
RP75
(11015)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(539)
Full
(5902)
Representative proteomes UniProt
(33529)
RP15
(914)
RP35
(2931)
RP55
(6054)
RP75
(11015)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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_888 (release 4.0)
Previous IDs: Amidase_4;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 539
Number in full: 5902
Average length of the domain: 134.6 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 33.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.2 30.2
Trusted cut-off 30.2 30.2
Noise cut-off 30.1 30.1
Model length: 86
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 Glucosaminidase domain has been found. There are 23 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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