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10  structures 737  species 3  interactions 1145  sequences 25  architectures

Family: Glyco_hydro_57 (PF03065)

Summary: Glycosyl hydrolase family 57

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This is the Wikipedia entry entitled "Glycoside hydrolase family 57". More...

Glycoside hydrolase family 57 Edit Wikipedia article

Glycosyl hydrolase family 57
Identifiers
Symbol Glyco_hydro_57
Pfam PF03065
Pfam clan CL0158
SCOP 1k1x
SUPERFAMILY 1k1x
CAZy GH57

In molecular biology, glycoside hydrolase family 57 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 57 CAZY GH_57 comprises enzymes with several known activities; alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), α-galactosidase (EC 3.2.1.22); amylopullulanase (EC 3.2.1.41); branching enzyme (EC 2.4.1.18). It includes a thermostable alpha-amylase with a broad substrate specificity from the archaebacterium Pyrococcus furiosus.[6]

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. ^ Laderman KA, Davis BR, Krutzsch HC, Lewis MS, Griko YV, Privalov PL et al. (1993). "The purification and characterization of an extremely thermostable alpha-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus.". J Biol Chem 268 (32): 24394–401. PMID 8226989. 

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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 57 Provide feedback

This family includes alpha-amylase ( EC:3.2.1.1), 4--glucanotransferase ( EC:2.4.1.-) and amylopullulanase enzymes.

Literature references

  1. Laderman KA, Davis BR, Krutzsch HC, Lewis MS, Griko YV, Privalov PL, Anfinsen CB; , J Biol Chem 1993;268:24394-24401.: The purification and characterization of an extremely thermostable alpha-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus. PUBMED:8226989 EPMC:8226989


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004300

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 57 CAZY comprises enzymes with two known activities; alpha-amylase (EC) and 4-alpha-glucanotransferase (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 GH_CE (CL0158), which has the following description:

This superfamily contains diverse enzymes that act on carbohydrates including both hydrolases and deacetylases.

The clan contains the following 6 members:

DUF2334 Glyco_hydro_38 Glyco_hydro_57 LamB_YcsF Polysacc_deac_1 Polysacc_deac_3

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
(22)
Full
(1145)
Representative proteomes NCBI
(1481)
Meta
(541)
RP15
(229)
RP35
(411)
RP55
(492)
RP75
(560)
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Format an alignment

  Seed
(22)
Full
(1145)
Representative proteomes NCBI
(1481)
Meta
(541)
RP15
(229)
RP35
(411)
RP55
(492)
RP75
(560)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(22)
Full
(1145)
Representative proteomes NCBI
(1481)
Meta
(541)
RP15
(229)
RP35
(411)
RP55
(492)
RP75
(560)
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_2506 (release 6.4)
Previous IDs: none
Type: Family
Author: Bateman A, Moxon SJ
Number in seed: 22
Number in full: 1145
Average length of the domain: 339.30 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 56.79 %

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 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 360
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

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

DUF1926 DUF1925 Glyco_hydro_57

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_57 domain has been found. There are 10 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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