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2  structures 264  species 3  interactions 586  sequences 29  architectures

Family: PRKCSH (PF07915)

Summary: Glucosidase II beta subunit-like protein

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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.

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.

Glucosidase II beta subunit-like protein Provide feedback

The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II (P14314), which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing [1]. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum [1]. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown [2]. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain.

Literature references

  1. Pelletier MF, Marcil A, Sevigny G, Jakob CA, Tessier DC, Chevet E, Menard R, Bergeron JJ, Thomas DY; , Glycobiology 2000;10:815-827.: The heterodimeric structure of glucosidase II is required for its activity, solubility, and localization in vivo. PUBMED:10929008 EPMC:10929008

  2. Li A, Davila S, Furu L, Qian Q, Tian X, Kamath PS, King BF, Torres VE, Somlo S; , Am J Hum Genet 2003;72:691-703.: Mutations in PRKCSH cause isolated autosomal dominant polycystic liver disease. PUBMED:12529853 EPMC:12529853


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012913

The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II (SWISSPROT), which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing [PUBMED:10929008]. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum [PUBMED:10929008]. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown [PUBMED:12529853].

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 M6PR (CL0226), which has the following description:

This clan includes cation dependent and independent mannose 6-phosphate receptors.

The clan contains the following 5 members:

ATG27 CIMR Man-6-P_recep PRKCSH PRKCSH_1

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(104)
Full
(586)
Representative proteomes NCBI
(860)
Meta
(7)
RP15
(128)
RP35
(189)
RP55
(295)
RP75
(365)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(104)
Full
(586)
Representative proteomes NCBI
(860)
Meta
(7)
RP15
(128)
RP35
(189)
RP55
(295)
RP75
(365)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(104)
Full
(586)
Representative proteomes NCBI
(860)
Meta
(7)
RP15
(128)
RP35
(189)
RP55
(295)
RP75
(365)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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.

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_9407 (release 14.0)
Previous IDs: none
Type: Family
Author: Fenech M
Number in seed: 104
Number in full: 586
Average length of the domain: 84.40 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 19.03 %

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 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.6 21.7
Model length: 81
Family (HMM) version: 8
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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Interactions

There are 3 interactions for this family. More...

TGF_beta Kazal_1 FOLN

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 PRKCSH domain has been found. There are 2 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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