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9  structures 534  species 2  interactions 820  sequences 13  architectures

Family: Glyco_hydro_108 (PF05838)

Summary: Glycosyl hydrolase 108

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This is the Wikipedia entry entitled "Glycoside hydrolase family 108". More...

Glycoside hydrolase family 108 Edit Wikipedia article

Glycosyl hydrolase 108
Symbol Glyco_hydro_108
Pfam PF05838
Pfam clan CL0037
CAZy GH108

In molecular biology, glycoside hydrolase family 108 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( web site,[4] and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.[5]

Glycoside hydrolase family 108 CAZY GH_108 includes enzymes with lysozyme (N-acetylmuramidase) EC activity. A glutamic acid residue within a conserved Glu-Gly-Gly-Tyr motif is essential for catalytic activity.[6] In bacteria, it may activate the secretion of large proteins via the breaking and rearrangement of the peptidoglycan layer during secretion.[7][8]


  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. 
  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. ^ Stojković EA, Rothman-Denes LB (2007). "Coliphage N4 N-acetylmuramidase defines a new family of murein hydrolases.". J Mol Biol 366 (2): 406–19. doi:10.1016/j.jmb.2006.11.028. PMID 17174325. 
  7. ^ Pei J, Grishin NV (2005). "COG3926 and COG5526: a tale of two new lysozyme-like protein families.". Protein Sci 14 (10): 2574–81. doi:10.1110/ps.051656805. PMC 2253296. PMID 16155206. 
  8. ^ Kondo Y, Toyoda A, Fukushi H, Yanase H, Tonomura K, Kawasaki H et al. (1994). "Cloning and characterization of a pair of genes that stimulate the production and secretion of Zymomonas mobilis extracellular levansucrase and invertase.". Biosci Biotechnol Biochem 58 (3): 526–30. doi:10.1271/bbb.58.526. PMID 7764692. 

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.

Glycosyl hydrolase 108 Provide feedback

This family acts as a lysozyme (N-acetylmuramidase), EC: It contains a conserved EGGY motif near the N-terminus, the glutamic acid within this motif is essential for catalytic activity [1]. In bacteria, it may activate the secretion of large proteins via the breaking and rearrangement of the peptidoglycan layer during secretion [2,3]. It is frequently found at the N-terminus of proteins containing a C-terminal PF09374 domain.

Literature references

  1. Stojkovic EA, Rothman-Denes LB;, J Mol Biol. 2007;366:406-419.: Coliphage N4 N-acetylmuramidase defines a new family of murein hydrolases. PUBMED:17174325 EPMC:17174325

  2. Pei J, Grishin NV; , Protein Sci 2005; [Epub ahead of print]: COG3926 and COG5526: A tale of two new lysozyme-like protein families. PUBMED:16155206 EPMC:16155206

  3. Kondo Y, Toyoda A, Fukushi H, Yanase H, Tonomura K, Kawasaki H, Sakai T;, Biosci Biotechnol Biochem. 1994;58:526-530.: Cloning and characterization of a pair of genes that stimulate the production and secretion of Zymomonas mobilis extracellular levansucrase and invertase. PUBMED:7764692 EPMC:7764692

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008565

This family consists of several hypothetical bacterial sequences as well as one viral sequence SWISSPROT, the function of this family is unknown.

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 12 members:

Glucosaminidase Glyco_hydro_108 Glyco_hydro_19 Glyco_hydro_46 Lys Lysozyme_like Phage_lysozyme REGB_T4 SLT SLT_2 TraH_2 Transglycosylas


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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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...


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_8737 (release 8.0)
Previous IDs: DUF847;
Type: Domain
Author: Moxon SJ, Bateman A, Eberhardt R
Number in seed: 20
Number in full: 820
Average length of the domain: 85.40 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 42.35 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 21.2
Trusted cut-off 21.4 21.6
Noise cut-off 20.1 20.8
Model length: 83
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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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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There are 2 interactions for this family. More...

PG_binding_3 Glyco_hydro_108


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 Glyco_hydro_108 domain has been found. There are 9 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 seqence.

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