Summary: Glycosyl hydrolase family 14
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Glycoside hydrolase family 14 Edit Wikipedia article
|Glycosyl hydrolase family 14|
beta-amylase from bacillus cereus var. mycoides in complex with maltose
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(http://www.cazy.org/GH1.html) web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Glycoside hydrolase family 14 CAZY GH_14 comprises enzymes with only one known activity; beta-amylase (EC 18.104.22.168). A Glu residue has been proposed as a catalytic residue, but it is not known if it is the nucleophile or the proton donor. Beta-amylase is an enzyme that hydrolyzes 1,4-alpha-glucosidic linkages in starch-type polysaccharide substrates so as to remove successive maltose units from the non-reducing ends of the chains. Beta-amylase is present in certain bacteria as well as in plants.
Three highly conserved sequence regions are found in all known beta-amylases. The first of these regions is located in the N-terminal section of the enzymes and contains an aspartate which is known to be involved in the catalytic mechanism. The second, located in a more central location, is centred around a glutamate which is also involved in the catalytic mechanism.
The 3D structure of a complex of soybean beta-amylase with an inhibitor (alpha-cyclodextrin) has been determined to 3.0A resolution by X-ray diffraction. The enzyme folds into large and small domains: the large domain has a (beta alpha)8 super-secondary structural core, while the smaller is formed from two long loops extending from the beta-3 and beta-4 strands of the (beta alpha)8 fold. The interface of the two domains, together with shorter loops from the (beta alpha)8 core, form a deep cleft, in which the inhibitor binds. Two maltose molecules also bind in the cleft, one sharing a binding site with alpha-cyclodextrin, and the other sitting more deeply in the cleft.
- 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.
- Henrissat, B. and Coutinho P.M. "Carbohydrate-Active Enzymes server". 1999.
- CAZypedia, an online encyclopedia of carbohydrate-active enzymes.
- Fukazawa C, Mikami B, Morita Y (1988). "Primary structure and function of beta-amylase". Seikagaku 60 (3): 211–216. PMID 2457058.
- Friedberg F, Rhodes C (1988). "Segments of amino acid sequence similarity in beta-amylases". Protein Seq. Data Anal. 1 (6): 499–501. PMID 2464171.
- Sakiyama F, Nitta Y, Isoda Y, Toda H (1989). "Identification of glutamic acid 186 affinity-labeled by 2,3-epoxypropyl alpha-D-glucopyranoside in soybean beta-amylase". J. Biochem. 105 (4): 573–576. PMID 2474529.
- Totsuka A, Nong VH, Kadokawa H, Itoh Y, Fukazawa C, Kim CS (1994). "Residues essential for catalytic activity of soybean beta-amylase". Eur. J. Biochem. 221 (2): 649–654. doi:10.1111/j.1432-1033.1994.tb18777.x. PMID 8174545.
- Katsube Y, Mikami B, Sato M, Shibata T, Hirose M, Aibara S, Morita Y (1992). "Three-dimensional structure of soybean beta-amylase determined at 3.0 A resolution: preliminary chain tracing of the complex with alpha-cyclodextrin". J. Biochem. 112 (4): 541–546. PMID 1491009.
Glycosyl hydrolase family 14 Provide feedback
This family are beta amylases.
Internal database links
|Similarity to PfamA using HHSearch:||Glyco_hydro_42|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001554
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) web site.
Glycoside hydrolase family 14 CAZY comprises enzymes with only one known activity; beta-amylase (EC). A Glu residue has been proposed as a catalytic residue, but it is not known if it is the nucleophile or the proton donor.
Beta-amylase [PUBMED:2457058, PUBMED:2464171] is an enzyme that hydrolyses 1,4-alpha-glucosidic linkages in starch-type polysaccharide substrates so as to remove successive maltose units from the non-reducing ends of the chains. Beta-amylase is present in certain bacteria as well as in plants.
Three highly conserved sequence regions are found in all known beta-amylases. The first of these regions is located in the N-terminal section of the enzymes and contains an aspartate which is known [PUBMED:2474529] to be involved in the catalytic mechanism. The second, located in a more central location, is centred around a glutamate which is also involved [PUBMED:8174545] in the catalytic mechanism.
The 3D structure of a complex of soybean beta-amylase with an inhibitor (alpha-cyclodextrin) has been determined to 3.0A resolution by X-ray diffraction [PUBMED:1491009]. The enzyme folds into large and small domains: the large domain has a (beta alpha)8 super-secondary structural core, while the smaller is formed from two long loops extending from the beta-3 and beta-4 strands of the (beta alpha)8 fold [PUBMED:1491009]. The interface of the two domains, together with shorter loops from the (beta alpha)8 core, form a deep cleft, in which the inhibitor binds [PUBMED:1491009]. Two maltose molecules also bind in the cleft, one sharing a binding site with alpha-cyclodextrin, and the other sitting more deeply in the cleft [PUBMED:1491009].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||beta-amylase activity (GO:0016161)|
|Biological process||polysaccharide catabolic process (GO:0000272)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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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 50 members:Alpha-amylase Alpha_L_fucos Cellulase Cellulase-like DUF187 DUF4015 DUF4038 DUF4434 GHL1-3 GHL12 GHL13 GHL15 GHL5 GHL6 Glyco_hydr_30_2 Glyco_hydro_1 Glyco_hydro_10 Glyco_hydro_101 Glyco_hydro_114 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_72 Glyco_hydro_77 Glyco_hydro_79n Glyco_hydro_97 Glyco_hydro_cc hDGE_amylase Lipid_bd Melibiase NAGidase NAGLU Raffinose_syn Xylanase
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Number in seed:||5|
|Number in full:||548|
|Average length of the domain:||308.80 aa|
|Average identity of full alignment:||44 %|
|Average coverage of the sequence by the domain:||78.16 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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_14 domain has been found. There are 66 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 seqence.
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