Summary: Glycosyl Hydrolase Family 88
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This is the Wikipedia entry entitled "Glycoside hydrolase family 88". More...
Glycoside hydrolase family 88 Edit Wikipedia article
Glycosyl Hydrolase Family 88 | |||||||||
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Identifiers | |||||||||
Symbol | Glyco_hydro_88 | ||||||||
Pfam | PF07470 | ||||||||
Pfam clan | CL0059 | ||||||||
SCOPe | 1nc5 / SUPFAM | ||||||||
CAZy | GH88 | ||||||||
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In molecular biology, glycoside hydrolase family 88 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 88 CAZY GH_88 includes enzymes with d-4,5 unsaturated β-glucuronyl hydrolase activity.[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 88". CAZypedia.org. Retrieved 2018-03-06.
- ^ CAZypedia Consortium (December 2018). "Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes". Glycobiology. 28 (1): 3–8. doi:10.1093/glycob/cwx089. PMID 29040563.
- ^ Hashimoto W, Kobayashi E, Nankai H, Sato N, Miya T, Kawai S, et al. (1999). "Unsaturated glucuronyl hydrolase of Bacillus sp. GL1: novel enzyme prerequisite for metabolism of unsaturated oligosaccharides produced by polysaccharide lyases". Arch Biochem Biophys. 368 (2): 367–74. doi:10.1006/abbi.1999.1305. PMID 10441389.
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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 88 Provide feedback
Unsaturated glucuronyl hydrolase catalyses the hydrolytic release of unsaturated glucuronic acids from oligosaccharides ( EC:3.2.1.-) produced by the reactions of polysaccharide lyases [1].
Literature references
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Mori S, Akao S, Miyake O, Nankai H, Hashimoto W, Mikami B, Murata K; , Acta Crystallogr D Biol Crystallogr 2003;59:946-949.: Crystallization and preliminary X-ray analysis of a novel unsaturated glucuronyl hydrolase from Bacillus sp. GL1. PUBMED:12777820 EPMC:12777820
Internal database links
SCOOP: | C5-epim_C GlcNAc_2-epim Glyco_hydro_127 Glyco_hydro_47 Glyco_hydro_76 LANC_like |
Similarity to PfamA using HHSearch: | Glyco_hydro_76 |
External database links
CAZY: | GH88 |
SCOP: | 1nc5 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR010905
Unsaturated glucuronyl hydrolase catalyses the hydrolytic release of unsaturated glucuronic acids from oligosaccharides produced by the reactions of polysaccharide lyases [PUBMED:12777820].
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 TrehalaseAlignments
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 (17) |
Full (6366) |
Representative proteomes | UniProt (21914) |
NCBI (31251) |
Meta (110) |
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RP15 (548) |
RP35 (2803) |
RP55 (5869) |
RP75 (10395) |
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HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (17) |
Full (6366) |
Representative proteomes | UniProt (21914) |
NCBI (31251) |
Meta (110) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (548) |
RP35 (2803) |
RP55 (5869) |
RP75 (10395) |
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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_10896 (release 10.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 17 |
Number in full: | 6366 |
Average length of the domain: | 327.50 aa |
Average identity of full alignment: | 17 % |
Average coverage of the sequence by the domain: | 76.44 % |
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: | 344 | ||||||||||||
Family (HMM) version: | 14 | ||||||||||||
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 is 1 interaction for this family. More...
Glyco_hydro_88Structures
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_88 domain has been found. There are 40 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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