Summary: Glycosyl hydrolases family 38 C-terminal beta sandwich domain
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This is the Wikipedia entry entitled "Glycoside hydrolase family 38". More...
Glycoside hydrolase family 38 Edit Wikipedia article
| Glycosyl hydrolases family 38 N-terminal domain | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 golgi alpha-mannosidase ii | |||||||||
| Identifiers | |||||||||
| Symbol | Glyco_hydro_38 | ||||||||
| Pfam | PF01074 | ||||||||
| Pfam clan | CL0158 | ||||||||
| InterPro | IPR000602 | ||||||||
| SCOPe | 1o7d / SUPFAM | ||||||||
| CAZy | GH38 | ||||||||
| Membranome | 311 | ||||||||
| |||||||||
| Alpha mannosidase, middle domain | |||||||||
|---|---|---|---|---|---|---|---|---|---|
golgi alpha-mannosidase ii | |||||||||
| Identifiers | |||||||||
| Symbol | Alpha-mann_mid | ||||||||
| Pfam | PF09261 | ||||||||
| InterPro | IPR015341 | ||||||||
| SCOPe | 1o7d / SUPFAM | ||||||||
| |||||||||
| Glycosyl hydrolases family 38 C-terminal domain | |||||||||
|---|---|---|---|---|---|---|---|---|---|
golgi alpha-mannosidase ii | |||||||||
| Identifiers | |||||||||
| Symbol | Glyco_hydro_38C | ||||||||
| Pfam | PF07748 | ||||||||
| Pfam clan | CL0103 | ||||||||
| InterPro | IPR011682 | ||||||||
| SCOPe | 1o7d / SUPFAM | ||||||||
| CAZy | GH38 | ||||||||
| |||||||||
In molecular biology, glycoside hydrolase family 38 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 38 CAZY GH_38 comprises enzymes with only one known activity; alpha-mannosidase (EC 3.2.1.24) (EC 3.2.1.114).
Lysosomal alpha-mannosidase is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. The enzyme catalyzes the hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides, and can cleave all known types of alpha-mannosidic linkages. Defects in the gene cause lysosomal alpha-mannosidosis (AM), a lysosomal storage disease characterised by the accumulation of unbranched oligo-saccharide chains.
A domain, which is found in the central region adopts a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. The domain is predominantly found in the enzyme alpha-mannosidase.[8]
References
- ^ 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.
- ^ 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.
- ^ 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.
- ^ "Home". CAZy.org. Retrieved 2018-03-06.
- ^ 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.
- ^ "Glycoside Hydrolase Family 38". CAZypedia.org. Retrieved 2018-03-06.
- ^ 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.
- ^ Heikinheimo P, Helland R, Leiros HK, Leiros I, Karlsen S, Evjen G, Ravelli R, Schoehn G, Ruigrok R, Tollersrud OK, McSweeney S, Hough E (March 2003). "The structure of bovine lysosomal alpha-mannosidase suggests a novel mechanism for low-pH activation". Journal of Molecular Biology. 327 (3): 631–44. doi:10.1016/S0022-2836(03)00172-4. PMID 12634058.
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Glycosyl hydrolases family 38 C-terminal beta sandwich domain Provide feedback
This domain is found at the C-terminal end of various glycosyl hydrolases belonging to family 38. The domain has a beta sandwich fold.
Literature references
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Henrissat B , Biochem Soc Trans 1998;26:153-156.: Glycosidase families PUBMED:9649738 EPMC:9649738
External database links
| CAZY: | GH38 |
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 GHD (CL0369), which has the following description:
This domain is C-terminal to the catalytic beta/alpha barrel domain. The superfamily includes the C-terminal domain of a number of sugar-lytic families.
The clan contains the following 39 members:
Alpha-amyl_C Alpha-amyl_C2 Alpha-amylase_C Alpha-L-AF_C AMPK1_CBM Bac_A_amyl_C BetaGal_dom2 CBM_20 CBM_48 Collagen_bind_2 Cyc-maltodext_C DUF1921 DUF1923 DUF1939 DUF1945 DUF1953 DUF1964 DUF1966 DUF3372 DUF3459 Fucosidase_C GH97_C GHD GlgX_C Glyc_hyd_38C_2 Glyco_hyd_101C Glyco_hydro38C2 Glyco_hydro_30C Glyco_hydro_36C Glyco_hydro_42C Glyco_hydro_5_C HepII_C hGDE_central Lact_bio_phlase LBP_C Malt_amylase_C Melibiase_2_C Melibiase_C SpuA_CAlignments
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 (147) |
Full (4054) |
Representative proteomes | UniProt (11595) |
NCBI (18873) |
Meta (32) |
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| RP15 (482) |
RP35 (1844) |
RP55 (3470) |
RP75 (5423) |
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| Jalview | |||||||||
| HTML | |||||||||
| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (147) |
Full (4054) |
Representative proteomes | UniProt (11595) |
NCBI (18873) |
Meta (32) |
||||
|---|---|---|---|---|---|---|---|---|---|
| RP15 (482) |
RP35 (1844) |
RP55 (3470) |
RP75 (5423) |
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| 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_731 (release 3.0) |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Finn RD  , Bateman A
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| Number in seed: | 147 |
| Number in full: | 4054 |
| Average length of the domain: | 86.80 aa |
| Average identity of full alignment: | 23 % |
| Average coverage of the sequence by the domain: | 8.86 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 69 | ||||||||||||
| Family (HMM) version: | 2 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Eukaryota
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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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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_hydro38C2 domain has been found. There are 13 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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