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11  structures 750  species 0  interactions 1500  sequences 33  architectures

Family: Glyco_hydr_116N (PF12215)

Summary: beta-glucosidase 2, glycosyl-hydrolase family 116 N-term

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beta-glucosidase 2, glycosyl-hydrolase family 116 N-term Provide feedback

This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 320 to 354 amino acids in length. This domain is found associated with PF04685. It is found just after the extreme N terminus. The N-terminal is thought to be the luminal domain while the C terminal is the cytosolic domain. The catalytic domain of GBA-2 is unknown. 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 [2,3]. The catalytic nucleophile, identified in UniProtKB:Q97YG8_SULSO is a glutamine-335 in the downstream family PF04685 [4].

Literature references

  1. 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

  2. Martin E, Schule R, Smets K, Rastetter A, Boukhris A, Loureiro JL, Gonzalez MA, Mundwiller E, Deconinck T, Wessner M, Jornea L, Oteyza AC, Durr A, Martin JJ, Schols L, Mhiri C, Lamari F, Zuchner S, De Jonghe P, Kabashi E, Brice A, Stevanin G;, Am J Hum Genet. 2013;92:238-244.: Loss of function of glucocerebrosidase GBA2 is responsible for motor neuron defects in hereditary spastic paraplegia. PUBMED:23332916 EPMC:23332916

  3. 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

  4. 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


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024462

This entry represents the N-terminal domain found in the CAZyme GH116 family members, which presently includes enzymes with beta-glucosidase (EC), beta-xylosidase (EC) , and glucocerebrosidase (EC) activity [PUBMED:23332917, PUBMED:20427274]. The N-terminal is thought to be the luminal domain while the C-terminal is the cytosolic domain.

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].

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 Gal_mutarotase (CL0103), which has the following description:

This clan is composed of a beta-sandwich that was first observed in domain 5 of beta-galactosidase, then as the central domain of copper amine oxidase, the C-terminal domain of chondroitinase, the C-terminal domain of hyaluronate lyase, the N-terminal domain of maltose phosphorylase and in Galactose Mutarotase [1]. All these enzymes act on a sugar substrate.

The clan contains the following 31 members:

Aldose_epim Bgal_small_N Cu_amine_oxid DUF1926 DUF4432 DUF4450 DUF4968 DUF5054 DUF5107 DUF5127 Gal_mutarotas_2 Gal_mutarotas_3 GH97_N Glucodextran_N Glyco_hyd_65N_2 Glyco_hydr_116N Glyco_hydro_36N Glyco_hydro_38 Glyco_hydro_38C Glyco_hydro_52 Glyco_hydro_65N Glyco_hydro_81 Glyco_hydro_92N Glyco_transf_36 Hepar_II_III Lyase_8 MdoG NtCtMGAM_N Rhamnogal_lyase RhgB_N YidC_periplas

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
(144)
Full
(1500)
Representative proteomes UniProt
(2449)
NCBI
(3224)
Meta
(61)
RP15
(401)
RP35
(898)
RP55
(1287)
RP75
(1537)
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PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(144)
Full
(1500)
Representative proteomes UniProt
(2449)
NCBI
(3224)
Meta
(61)
RP15
(401)
RP35
(898)
RP55
(1287)
RP75
(1537)
Alignment:
Format:
Order:
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
(144)
Full
(1500)
Representative proteomes UniProt
(2449)
NCBI
(3224)
Meta
(61)
RP15
(401)
RP35
(898)
RP55
(1287)
RP75
(1537)
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_2416 (release 23.0)
Previous IDs: GBA2_N;
Type: Family
Sequence Ontology: SO:0100021
Author: Assefa S , Gavin OL
Number in seed: 144
Number in full: 1500
Average length of the domain: 278.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 35.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.2 30.2
Trusted cut-off 30.2 30.5
Noise cut-off 29.8 29.9
Model length: 312
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

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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 Glyco_hydr_116N 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.

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