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16  structures 1317  species 3  interactions 2515  sequences 24  architectures

Family: Glyco_hydro_15 (PF00723)

Summary: Glycosyl hydrolases family 15

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This is the Wikipedia entry entitled "Glycoside hydrolase family 15". More...

Glycoside hydrolase family 15 Edit Wikipedia article

Glycosyl hydrolases family 15
Identifiers
Symbol Glyco_hydro_15
Pfam PF00723
Pfam clan CL0059
SCOP 1glm
SUPERFAMILY 1glm
CAZy GH15

In molecular biology, glycoside hydrolase family 15 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(http://www.cazy.org/GH1.html) web site,[4] and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.[5]

Glycoside hydrolase family 15 CAZY GH_15 comprises enzymes with several known activities; glucoamylase (EC 3.2.1.3); alpha-glucosidase (EC 3.2.1.20); glucodextranase (EC 3.2.1.70).

Glucoamylase (GA) catalyses the release of D-glucose from the non-reducing ends of starch and other oligo- or poly-saccharides. Studies of fungal GA have indicated 3 closely clustered acidic residues that play a role in the catalytic mechanism.[6] This region is also conserved in a recently sequenced bacterial GA.[7]

The 3D structure of the pseudo-tetrasaccharide acarbose complexed with glucoamylase II(471) from Aspergillus awamori var. X100 has been determined to 2.4A resolution.[8] The protein belongs to the mainly alpha class, and contains 19 helices and 9 strands.

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ Bairoch, A. "Classification of glycosyl hydrolase families and index of glycosyl hydrolase entries in SWISS-PROT". 1999.
  4. ^ Henrissat, B. and Coutinho P.M. "Carbohydrate-Active Enzymes server". 1999.
  5. ^ CAZypedia, an online encyclopedia of carbohydrate-active enzymes.
  6. ^ Svensson B, Ford C, Sierks MR, Reilly PJ (1990). "Catalytic mechanism of fungal glucoamylase as defined by mutagenesis of Asp176, Glu179 and Glu180 in the enzyme from Aspergillus awamori". Protein Eng. 3 (3): 193–198. doi:10.1093/protein/3.3.193. PMID 1970434. 
  7. ^ Ohnishi H, Kitamura H, Minowa T, Sakai H, Ohta T (1992). "Molecular cloning of a glucoamylase gene from a thermophilic Clostridium and kinetics of the cloned enzyme". Eur. J. Biochem. 207 (2): 413–418. doi:10.1111/j.1432-1033.1992.tb17064.x. PMID 1633799. 
  8. ^ Aleshin AE, Firsov LM, Honzatko RB (1994). "Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution". J. Biol. Chem. 269 (22): 15631–15639. PMID 8195212. 

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Glycosyl hydrolases family 15 Provide feedback

In higher organisms this family is represented by phosphorylase kinase subunits.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011613

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 15 CAZY comprises enzymes with several known activities; glucoamylase (EC); alpha-glucosidase (EC); glucodextranase (EC).

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 28 members:

A2M_comp Bac_rhamnosid C5-epim_C Cobalamin_bind DUF1237 DUF1680 DUF2807 DUF4097 DUF4098 DUF608 GDE_C GlcNAc_2-epim Glyco_hydro_100 Glyco_hydro_15 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 Pec_lyase Prenyltrans Prenyltrans_1 Prenyltrans_2 Trehalase

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(26)
Full
(2515)
Representative proteomes NCBI
(2459)
Meta
(281)
RP15
(366)
RP35
(666)
RP55
(954)
RP75
(1160)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(26)
Full
(2515)
Representative proteomes NCBI
(2459)
Meta
(281)
RP15
(366)
RP35
(666)
RP55
(954)
RP75
(1160)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(26)
Full
(2515)
Representative proteomes NCBI
(2459)
Meta
(281)
RP15
(366)
RP35
(666)
RP55
(954)
RP75
(1160)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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 View help on the curation process

Seed source: Pfam-B_771 (release 2.1)
Previous IDs: glycosyl_hydr10;
Type: Family
Author: Bateman A
Number in seed: 26
Number in full: 2515
Average length of the domain: 390.30 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 61.49 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 21.8 21.7
Noise cut-off 21.3 21.6
Model length: 448
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

Glyco_hydro_15 Glucodextran_B Glucodextran_N

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_15 domain has been found. There are 16 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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