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5  structures 1312  species 0  interactions 1669  sequences 49  architectures

Family: Glyco_hydro_63N (PF16923)

Summary: Glycosyl hydrolase family 63 N-terminal domain

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 63". More...

Glycoside hydrolase family 63 Edit Wikipedia article

Mannosyl oligosaccharide glucosidase
Identifiers
SymbolGlyco_hydro_63
PfamPF03200
Pfam clanCL0059
InterProIPR004888
CAZyGH63

In molecular biology, glycoside hydrolase family 63 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]

Glycosyl hydrolase family 63 (CAZY GH_63) is a family of eukaryotic enzymes. They catalyse the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide glucosidase EC 3.2.1.106 is the first enzyme in the N-linked oligosaccharide processing pathway.

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.
This article incorporates text from the public domain Pfam and InterPro: IPR004888

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 family 63 N-terminal domain Provide feedback

This is a family of eukaryotic enzymes belonging to glycosyl hydrolase family 63. They catalyse the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide glucosidase EC:3.2.1.106 is the first enzyme in the N-linked oligosaccharide processing pathway. This family represents the N-terminal beta sandwich domain [1].

Literature references

  1. Barker MK, Rose DR;, J Biol Chem. 2013;288:13563-13574.: Specificity of Processing alpha-glucosidase I is guided by the substrate conformation: crystallographic and in silico studies. PUBMED:23536181 EPMC:23536181


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR031631

Glycoside hydrolases 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. More than 100 different families of glycoside hydrolases have been defined based on sequence similarity.

This entry represents the N-terminal beta sandwich domain found in glycosyl hydrolase family 63 proteins [ PUBMED:23536181 ]. Glycosyl hydrolase family 63 is a family of eukaryotic enzymes that catalyse the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2).

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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
(69)
Full
(1669)
Representative proteomes UniProt
(2762)
RP15
(345)
RP35
(807)
RP55
(1281)
RP75
(1719)
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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
(69)
Full
(1669)
Representative proteomes UniProt
(2762)
RP15
(345)
RP35
(807)
RP55
(1281)
RP75
(1719)
Alignment:
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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
(69)
Full
(1669)
Representative proteomes UniProt
(2762)
RP15
(345)
RP35
(807)
RP55
(1281)
RP75
(1719)
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_2589 (release 6.5)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mifsud W , Bateman A
Number in seed: 69
Number in full: 1669
Average length of the domain: 202.3 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 25.73 %

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 23.8 23.8
Trusted cut-off 24.3 24.0
Noise cut-off 23.3 23.2
Model length: 227
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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_hydro_63N domain has been found. There are 5 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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AlphaFold Structure Predictions