Summary: Glycoside hydrolase 97
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This is the Wikipedia entry entitled "Glycoside hydrolase family 97". More...
Glycoside hydrolase family 97 Edit Wikipedia article
| Glycoside hydrolase 97 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | Glyco_hydro_97 | ||||||||
| Pfam | PF10566 | ||||||||
| Pfam clan | CL0058 | ||||||||
| InterPro | IPR019563 | ||||||||
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In molecular biology, glycoside hydrolase family 97 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 97 (GH97) is a bacterial family. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands.[8]
External links
References
- ^ 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.
- ^ 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.
- ^ Bairoch, A. "Classification of glycosyl hydrolase families and index of glycosyl hydrolase entries in SWISS-PROT". 1999.
- ^ "Home". CAZy.org. Retrieved 2018-03-06.
- ^ Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie; Coutinho, Pedro M.; Henrissat, Bernard (2014-01-01). "The carbohydrate-active enzymes database (CAZy) in 2013". Nucleic Acids Research. 42 (D1): D490–D495. doi:10.1093/nar/gkt1178. ISSN 0305-1048. PMC 3965031. PMID 24270786.
- ^ "Glycoside Hydrolase Family 97". CAZypedia.org. Retrieved 2018-03-06.
- ^ CAZypedia Consortium (2018-12-01). "Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes". Glycobiology. 28 (1): 3–8. doi:10.1093/glycob/cwx089. hdl:21.11116/0000-0003-B7EB-6. ISSN 1460-2423. PMID 29040563.
- ^ Naumoff DG (2005). "GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily". BMC Genomics. 6: 112. doi:10.1186/1471-2164-6-112. PMC 1249566. PMID 16131397.
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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.
Glycoside hydrolase 97 Provide feedback
This domain is the catalytic region of the bacterial glycosyl-hydrolase family 97. This central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, form two additional non-catalytic domains [1]. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands [2,3].
Literature references
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Naumoff DG; , BMC Genomics. 2005;6:112.: GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily. PUBMED:16131397 EPMC:16131397
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Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ;, Chem Biol. 2008;15:1058-1067.: Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. PUBMED:18848471 EPMC:18848471
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Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M;, J Biol Chem. 2008;283:36328-36337.: Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. PUBMED:18981178 EPMC:18981178
Internal database links
| SCOOP: | AP_endonuc_2 Cellulase Glyco_hydro_31 Melibiase Melibiase_2 OrfB_IS605 OrfB_Zn_ribbon |
| Similarity to PfamA using HHSearch: | DUF871 |
External database links
| CAZY: | GH97 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR019563
Proteins containing this domain include the aglycoside hydrolase family 97 enzyme, SusB protein, from Bacteroides thetaiotaomicron. SusB has three domains: the N-terminal, catalytic, and C-terminal domains. This entry represents the catalytic domain that consists of a complete (beta/alpha)8-barrel or TIM-barrel. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, form two additional non-catalytic domains [PUBMED:18848471]. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands [PUBMED:18848471, PUBMED:18981178].
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 Glyco_hydro_tim (CL0058), which has the following description:
This large superfamily contains a range of glycosyl hydrolase enzymes that possess a TIM barrel fold. This CLAN merges clans GH-A, GH-D, GH-H and GH-K from CAZy.
The clan contains the following 57 members:
Alpha-amylase Alpha_L_fucos Cellulase Cellulase-like Dehydratase_LU DUF1906 DUF4015 DUF4038 DUF4434 DUF4838 DUF4849 DUF5010 GHL10 GHL13 GHL15 GHL5 GHL6 Glyco_hydr_30_2 Glyco_hydro_1 Glyco_hydro_10 Glyco_hydro_101 Glyco_hydro_114 Glyco_hydro_129 Glyco_hydro_14 Glyco_hydro_17 Glyco_hydro_18 Glyco_hydro_20 Glyco_hydro_25 Glyco_hydro_26 Glyco_hydro_2_C Glyco_hydro_3 Glyco_hydro_30 Glyco_hydro_31 Glyco_hydro_35 Glyco_hydro_39 Glyco_hydro_42 Glyco_hydro_44 Glyco_hydro_53 Glyco_hydro_56 Glyco_hydro_59 Glyco_hydro_66 Glyco_hydro_70 Glyco_hydro_71 Glyco_hydro_72 Glyco_hydro_77 Glyco_hydro_79n Glyco_hydro_85 Glyco_hydro_97 Glyco_hydro_99 Glyco_hydro_cc Glyco_tran_WbsX hDGE_amylase Melibiase Melibiase_2 NAGidase NAGLU Raffinose_synAlignments
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 (87) |
Full (2327) |
Representative proteomes | UniProt (5766) |
NCBI (7828) |
Meta (182) |
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| RP15 (363) |
RP35 (1269) |
RP55 (2331) |
RP75 (3585) |
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| 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 (87) |
Full (2327) |
Representative proteomes | UniProt (5766) |
NCBI (7828) |
Meta (182) |
||||
|---|---|---|---|---|---|---|---|---|---|
| RP15 (363) |
RP35 (1269) |
RP55 (2331) |
RP75 (3585) |
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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: | Naumoff D |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Coggill P 
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| Number in seed: | 87 |
| Number in full: | 2327 |
| Average length of the domain: | 271.30 aa |
| Average identity of full alignment: | 35 % |
| Average coverage of the sequence by the domain: | 39.58 % |
HMM information
| HMM build commands: |
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 281 | ||||||||||||
| Family (HMM) version: | 9 | ||||||||||||
| 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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Viruses
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Unclassified sequence
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Interactions
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_97 domain has been found. There are 24 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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