Summary: Glycosyl-hydrolase family 116, catalytic region
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.
Glycosyl-hydrolase family 116, catalytic region Provide feedback
This represents a family of archaeal, bacterial and eukaryotic glycosyl hydrolases, that belong to superfamily GH116. The primary catabolic pathway for glucosylceramide is catalysis by the lysosomal enzyme glucocerebrosidase. In higher eukaryotes, glucosylceramide is the precursor of glycosphingolipids, a complex group of ubiquitous membrane lipids [1]. Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia [3]. The catalytic nucleophile, identified in UniProtKB:Q97YG8_SULSO is a glutamine-335, with the likely acid/base at Asp-442 and the aspartates at Asp-406 and Asp-458 residues also playing a role in the catalysis of glucosides and xylosides that are beta-bound to hydrophobic groups. The family is defined as GH116, which presently includes enzymes with beta-glucosidase, EC:3.2.1.21, beta-xylosidase, EC:3.2.1.37, and glucocerebrosidase EC:3.2.1.45 activity [1,2].
Literature references
-
Boot RG, Verhoek M, Donker-Koopman W, Strijland A, van Marle J, Overkleeft HS, Wennekes T, Aerts JM;, J Biol Chem. 2007;282:1305-1312.: Identification of the non-lysosomal glucosylceramidase as beta-glucosidase 2. PUBMED:17105727 EPMC:17105727
-
Cobucci-Ponzano B, Aurilia V, Riccio G, Henrissat B, Coutinho PM, Strazzulli A, Padula A, Corsaro MM, Pieretti G, Pocsfalvi G, Fiume I, Cannio R, Rossi M, Moracci M;, J Biol Chem. 2010;285:20691-20703.: A new archaeal beta-glycosidase from Sulfolobus solfataricus: seeding a novel retaining beta-glycan-specific glycoside hydrolase family along with the human non-lysosomal glucosylceramidase GBA2. PUBMED:20427274 EPMC:20427274
-
Hammer MB, Eleuch-Fayache G, Schottlaender LV, Nehdi H, Gibbs JR, Arepalli SK, Chong SB, Hernandez DG, Sailer A, Liu G, Mistry PK, Cai H, Shrader G, Sassi C, Bouhlal Y, Houlden H, Hentati F, Amouri R, Singleton AB;, Am J Hum Genet. 2013;92:245-251.: Mutations in GBA2 cause autosomal-recessive cerebellar ataxia with spasticity. PUBMED:23332917 EPMC:23332917
Internal database links
SCOOP: | Bac_rhamnosid6H GDE_C Glyco_hydro_15 Glyco_hydro_36 Trehalase |
Similarity to PfamA using HHSearch: | GDE_C Bac_rhamnosid6H |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006775
This entry represents the catalytic region found in the CAZyme GH116 family members, which presently includes enzymes with beta-glucosidase (EC), beta-xylosidase (EC) , and glucocerebrosidase (EC) activity [PUBMED:20427274]. Proteins containing this domain include animal non-lysosomal glucosylceramidase GBA2, which catalyse the conversion of glucosylceramide to free glucose and ceramide [PUBMED:17105727]. GBA2 is involved in sphingomyelin generation and prevention of glycolipid accumulation and may also catalyse the hydrolysis of bile acid 3-O-glucosides, however, the relevance of such activity is unclear in vivo [PUBMED:17080196]. Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia [PUBMED:23332917]. The catalytic nucleophile, identified in SWISSPROT is a glutamine-335, with the likely acid/base at Asp-442 and the aspartates at Asp-406 and Asp-458 residues also playing a role in the catalysis of glucosides and xylosides that are beta-bound to hydrophobic groups [PUBMED:20427274].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
Pfam Clan
This family is a member of clan 6_Hairpin (CL0059), which has the following description:
This Clan includes CAZy clans GH-L, GH-M and GH-G. The members of this clan share a common structure composed of 6 helical hairpins. Most members of this superfamily are glycosyl hydrolase enzymes.
The clan contains the following 29 members:
Bac_rhamnosid6H C5-epim_C Cobalamin_bind DUF608 GDE_C GlcNAc_2-epim Glyco_hydro81C Glyco_hydro_100 Glyco_hydro_125 Glyco_hydro_127 Glyco_hydro_15 Glyco_hydro_36 Glyco_hydro_47 Glyco_hydro_48 Glyco_hydro_63 Glyco_hydro_65m Glyco_hydro_76 Glyco_hydro_8 Glyco_hydro_88 Glyco_hydro_9 Glycoamylase LANC_like Ldi Pec_lyase Prenyltrans SQHop_cyclase_C SQHop_cyclase_N TED_complement TrehalaseAlignments
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...
View options
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 (35) |
Full (1764) |
Representative proteomes | UniProt (4176) |
NCBI (6057) |
Meta (58) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (241) |
RP35 (874) |
RP55 (1548) |
RP75 (2182) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
Download options
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 (35) |
Full (1764) |
Representative proteomes | UniProt (4176) |
NCBI (6057) |
Meta (58) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (241) |
RP35 (874) |
RP55 (1548) |
RP75 (2182) |
||||||
Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_5657 (release 7.5) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Mifsud W |
Number in seed: | 35 |
Number in full: | 1764 |
Average length of the domain: | 322.10 aa |
Average identity of full alignment: | 37 % |
Average coverage of the sequence by the domain: | 39.61 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 361 | ||||||||||||
Family (HMM) version: | 14 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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 DUF608 domain has been found. There are 11 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.
Loading structure mapping...