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32  structures 1462  species 0  interactions 11217  sequences 189  architectures

Family: Glyco_hydro_47 (PF01532)

Summary: Glycosyl hydrolase family 47

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 47". More...

Glycoside hydrolase family 47 Edit Wikipedia article

Glycosyl hydrolase family 47
Identifiers
SymbolGlyco_hydro_47
PfamPF01532
Pfam clanCL0059
SCOPe1dl2 / SUPFAM
CAZyGH47
Membranome526

In molecular biology, glycoside hydrolase family 47 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][5] and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.[6][7]

Glycoside hydrolase family 47 CAZY GH_47 comprises enzymes with only one known activity; alpha-mannosidase (EC 3.2.1.113).

Alpha-mannosidase is involved in the maturation of Asn-linked oligosaccharides.[8] The enzyme hydrolyses terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide man(9)(glcnac)(2) in a calcium-dependent manner. The mannose residues are trimmed away to produce, first, man(8)glcnac(2), then a man(5)(glcnac)(2) structure.

References

  1. ^ Henrissat B, Callebaut I, Fabrega S, Lehn P, Mornon JP, Davies G (July 1995). "Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases". Proceedings of the National Academy of Sciences of the United States of America. 92 (15): 7090–4. doi:10.1073/pnas.92.15.7090. PMC 41477. PMID 7624375.
  2. ^ Davies G, Henrissat B (September 1995). "Structures and mechanisms of glycosyl hydrolases". Structure. 3 (9): 853–9. doi:10.1016/S0969-2126(01)00220-9. PMID 8535779.
  3. ^ Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical Journal. 316 (Pt 2): 695–6. doi:10.1042/bj3160695. PMC 1217404. PMID 8687420.
  4. ^ "Home". CAZy.org. Retrieved 2018-03-06.
  5. ^ Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (January 2014). "The carbohydrate-active enzymes database (CAZy) in 2013". Nucleic Acids Research. 42 (Database issue): D490–5. doi:10.1093/nar/gkt1178. PMC 3965031. PMID 24270786.
  6. ^ "Glycoside Hydrolase Family 47". CAZypedia.org. Retrieved 2018-03-06.
  7. ^ CAZypedia Consortium (December 2018). "Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes" (PDF). Glycobiology. 28 (1): 3–8. doi:10.1093/glycob/cwx089. PMID 29040563.
  8. ^ Lal A, Schutzbach JS, Forsee WT, Neame PJ, Moremen KW (April 1994). "Isolation and expression of murine and rabbit cDNAs encoding an alpha 1,2-mannosidase involved in the processing of asparagine-linked oligosaccharides". The Journal of Biological Chemistry. 269 (13): 9872–81. PMID 8144580.

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 47 Provide feedback

Members of this family are alpha-mannosidases that catalyse the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2).

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001382

O-Glycosyl hydrolases ( EC ) 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 glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [ PUBMED:7624375 , PUBMED:8535779 ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

Glycoside hydrolase family 47 CAZY comprises enzymes with only one known activity; alpha-mannosidase ( EC ).

Alpha-mannosidase is involved in the maturation of Asn-linked oligo-saccharides [ PUBMED:8144580 ]. The enzyme hydrolyses terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide man(9)(glcnac)(2) in a calcium-dependent manner. The mannose residues are trimmed away to produce, first, man(8)glcnac(2), then a man(5)(glcnac)(2) structure.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 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 Trehalase

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...

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
(97)
Full
(11217)
Representative proteomes UniProt
(20212)
RP15
(2094)
RP35
(5259)
RP55
(9024)
RP75
(11878)
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HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(97)
Full
(11217)
Representative proteomes UniProt
(20212)
RP15
(2094)
RP35
(5259)
RP55
(9024)
RP75
(11878)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(97)
Full
(11217)
Representative proteomes UniProt
(20212)
RP15
(2094)
RP35
(5259)
RP55
(9024)
RP75
(11878)
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_958 (release 4.0)
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Bateman A
Number in seed: 97
Number in full: 11217
Average length of the domain: 403.30 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 68.16 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.9 22.9
Trusted cut-off 22.9 22.9
Noise cut-off 22.8 22.8
Model length: 458
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Selections

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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_47 domain has been found. There are 32 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

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JW29 View 3D Structure Click here
A0A0R0GKX7 View 3D Structure Click here
A0A0R0JQE5 View 3D Structure Click here
A0A0R4IAP0 View 3D Structure Click here
A0A140LGE1 View 3D Structure Click here
A0A1D6EBC4 View 3D Structure Click here
A0A1D6HJW5 View 3D Structure Click here
A0A1D6HUB9 View 3D Structure Click here
A0A1D6HUB9 View 3D Structure Click here
A0A1D6J715 View 3D Structure Click here
A0A1D6KL44 View 3D Structure Click here
A0A1D8PD38 View 3D Structure Click here
A0A1D8PH01 View 3D Structure Click here
A0A2R8QLV1 View 3D Structure Click here
A2AJ15 View 3D Structure Click here
A5WWD5 View 3D Structure Click here
B0V2X9 View 3D Structure Click here
B2GUY0 View 3D Structure Click here
B6SH10 View 3D Structure Click here
C0PHV7 View 3D Structure Click here
D3Z979 View 3D Structure Click here
D3ZJE0 View 3D Structure Click here
D3ZR49 View 3D Structure Click here
E7F4N5 View 3D Structure Click here
E7F7X8 View 3D Structure Click here
E9QJF1 View 3D Structure Click here
F1Q540 View 3D Structure Click here
I1KGP3 View 3D Structure Click here
I1LC43 View 3D Structure Click here
I1M1F2 View 3D Structure Click here
I1MF37 View 3D Structure Click here
I1MTK9 View 3D Structure Click here
K7KPF4 View 3D Structure Click here
K7MK43 View 3D Structure Click here
K7TW48 View 3D Structure Click here
K7UWA5 View 3D Structure Click here
M9PG98 View 3D Structure Click here
O60476 View 3D Structure Click here
O94726 View 3D Structure Click here
P32906 View 3D Structure Click here
P33908 View 3D Structure Click here
P38888 View 3D Structure Click here
P39098 View 3D Structure Click here
P45700 View 3D Structure Click here
P53624 View 3D Structure Click here
P90787 View 3D Structure Click here
P90830 View 3D Structure Click here
Q09641 View 3D Structure Click here
Q0DK00 View 3D Structure Click here
Q0JIW3 View 3D Structure Click here
Q12205 View 3D Structure Click here
Q18679 View 3D Structure Click here
Q18788 View 3D Structure Click here
Q22120 View 3D Structure Click here
Q23296 View 3D Structure Click here
Q2HXL6 View 3D Structure Click here
Q4CL13 View 3D Structure Click here
Q4CL14 View 3D Structure Click here
Q4CMF3 View 3D Structure Click here
Q4CMR8 View 3D Structure Click here
Q4CN61 View 3D Structure Click here
Q4CRR9 View 3D Structure Click here
Q4D223 View 3D Structure Click here
Q4DC54 View 3D Structure Click here
Q4DC55 View 3D Structure Click here
Q4DC56 View 3D Structure Click here
Q4DCE0 View 3D Structure Click here
Q4DCT8 View 3D Structure Click here
Q4DK86 View 3D Structure Click here
Q54CH4 View 3D Structure Click here
Q54PP9 View 3D Structure Click here
Q54PQ0 View 3D Structure Click here
Q54PQ1 View 3D Structure Click here
Q550P3 View 3D Structure Click here
Q55EU0 View 3D Structure Click here
Q5RHM7 View 3D Structure Click here
Q6AYI8 View 3D Structure Click here
Q6NXK9 View 3D Structure Click here
Q6Z7S1 View 3D Structure Click here
Q7X6B1 View 3D Structure Click here
Q8BJT9 View 3D Structure Click here
Q8H116 View 3D Structure Click here
Q8IMK0 View 3D Structure Click here
Q925U4 View 3D Structure Click here
Q92611 View 3D Structure Click here
Q93Y37 View 3D Structure Click here
Q9BV94 View 3D Structure Click here
Q9BZQ6 View 3D Structure Click here
Q9C512 View 3D Structure Click here
Q9FG93 View 3D Structure Click here
Q9NR34 View 3D Structure Click here
Q9P7C3 View 3D Structure Click here
Q9SEH8 View 3D Structure Click here
Q9SXC9 View 3D Structure Click here
Q9UKM7 View 3D Structure Click here
Q9VAP8 View 3D Structure Click here
Q9VK27 View 3D Structure Click here