Summary: Glycosyl hydrolases family 38 N-terminal domain
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Glycoside hydrolase family 38 Edit Wikipedia article
|Glycosyl hydrolases family 38 N-terminal domain|
|SCOP2||1o7d / SCOPe / SUPFAM|
|Alpha mannosidase, middle domain|
|SCOP2||1o7d / SCOPe / SUPFAM|
|Glycosyl hydrolases family 38 C-terminal domain|
|SCOP2||1o7d / SCOPe / SUPFAM|
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. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
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.
- 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): 7090â€“4. Bibcode:1995PNAS...92.7090H. doi:10.1073/pnas.92.15.7090. PMCÂ 41477. PMIDÂ 7624375.
- Davies G, Henrissat B (September 1995). "Structures and mechanisms of glycosyl hydrolases". Structure. 3 (9): 853â€“9. doi:10.1016/S0969-2126(01)00220-9. PMIDÂ 8535779.
- Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical Journal. 316 (Pt 2): 695â€“6. doi:10.1042/bj3160695. PMCÂ 1217404. PMIDÂ 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. PMCÂ 3965031. PMIDÂ 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): 3â€“8. doi:10.1093/glycob/cwx089. PMIDÂ 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): 631â€“44. doi:10.1016/S0022-2836(03)00172-4. PMIDÂ 12634058.
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Glycosyl hydrolases family 38 N-terminal domain Provide feedback
Glycosyl hydrolases are key enzymes of carbohydrate metabolism.
Internal database links
|SCOOP:||Alpha-mann_mid Glyco_hydro_57 Polysacc_deac_1|
|Similarity to PfamA using HHSearch:||Glyco_hydro_57|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000602
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.
Lysosomal alpha-mannosidase is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. The enzyme catalyses 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.
This entry represents the N-terminal domain of the glycoside hydrolase 38 family protein.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||alpha-mannosidase activity (GO:0004559)|
|Biological process||mannose metabolic process (GO:0006013)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This superfamily contains diverse enzymes that act on carbohydrates including both hydrolases and deacetylases.
The clan contains the following 11 members:DUF2194 DUF2334 DUF3863 Glyco_hydro_38N Glyco_hydro_57 GxGYxYP_C LamB_YcsF Polysacc_deac_1 Polysacc_deac_2 Polysacc_deac_3 YdjC
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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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.
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Curation and family details
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|Seed source:||Pfam-B_731 (release 3.0)|
|Previous IDs:||Glycosyl_hydr16; Glyco_hydro_38;|
|Author:||Finn RD , Bateman A|
|Number in seed:||44|
|Number in full:||9723|
|Average length of the domain:||273.20 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||28.57 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||25|
|Download:||download the raw HMM for this family|
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How the sunburst is generated
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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_38N domain has been found. There are 89 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.