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473  structures 4623  species 17  interactions 28372  sequences 300  architectures

Family: Alpha-amylase (PF00128)

Summary: Alpha amylase, catalytic domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Alpha-Amylase". More...

Alpha-Amylase Edit Wikipedia article

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This is the Wikipedia entry entitled "Glycoside hydrolase family 13". More...

Glycoside hydrolase family 13 Edit Wikipedia article

Alpha amylase, N-terminal ig-like domain
PDB 2d0h EBI.jpg
crystal structure of thermoactinomyces vulgaris r-47 alpha-amylase 1 (tvai) mutant d356n/e396q complexed with p2, a pullulan model oligosaccharide
Identifiers
Symbol Alpha-amylase_N
Pfam PF02903
InterPro IPR004185
SCOP 1sma
SUPERFAMILY 1sma
Alpha-amylase catalytic domain
PDB 1cyg EBI.jpg
cyclodextrin glucanotransferase (e.c.2.4.1.19) (cgtase)
Identifiers
Symbol Alpha-amylase
Pfam PF00128
Pfam clan CL0058
InterPro IPR006047
SCOP 1ppi
SUPERFAMILY 1ppi
CAZy GH13

In molecular biology, glycoside hydrolase family 13 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]

Enzymes containing this domain belong to family 13 (CAZY GH_13) of the glycosyl hydrolases. The maltogenic alpha-amylase is an enzyme which catalyses hydrolysis of (1-4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains in the conversion of starch to maltose. Other enzymes in this family include neopullulanase, which hydrolyses pullulan to panose, and cyclomaltodextrinase, which hydrolyses cyclodextrins.

References[edit]

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.

Alpha amylase, catalytic domain Provide feedback

Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.

Literature references

  1. Larson SB, Greenwood A, Cascio D, Day J, McPherson A; , J Mol Biol 1994;235:1560-1584.: Refined molecular structure of pig pancreatic alpha-amylase at 2.1 A resolution. PUBMED:8107092 EPMC:8107092

  2. Strobl S, Maskos K, Betz M, Wiegand G, Huber R, Gomis-Ruth FX, Glockshuber R; , J Mol Biol 1998;278:617-628.: Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution. PUBMED:9600843 EPMC:9600843


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006047

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.

Enzymes containing this domain, such as alpha-amylase, belong to family 13 (CAZY) of the glycosyl hydrolases. The maltogenic alpha-amylase is an enzyme which catalyses hydrolysis of (1-4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains in the conversion of starch to maltose. Other enzymes include neopullulanase, which hydrolyses pullulan to panose, and cyclomaltodextrinase, which hydrolyses cyclodextrins.

This entry represents the catalytic domain found in several protein members of this family. It has a structure consisting of an 8 stranded alpha/beta barrel that contains the active site, interrupted by a ~70 amino acid calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain [PUBMED:16302977].

More information about this protein can be found at Protein of the Month: alpha-Amylase [PUBMED:].

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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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...

View options

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
(31)
Full
(28372)
Representative proteomes NCBI
(23482)
Meta
(3056)
RP15
(2088)
RP35
(4020)
RP55
(5641)
RP75
(6746)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(31)
Full
(28372)
Representative proteomes NCBI
(23482)
Meta
(3056)
RP15
(2088)
RP35
(4020)
RP55
(5641)
RP75
(6746)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(31)
Full
(28372)
Representative proteomes NCBI
(23482)
Meta
(3056)
RP15
(2088)
RP35
(4020)
RP55
(5641)
RP75
(6746)
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: Swissprot
Previous IDs: alpha-amylase;
Type: Domain
Author: Sonnhammer ELL, Griffiths-Jones SR
Number in seed: 31
Number in full: 28372
Average length of the domain: 261.10 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 44.76 %

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 20.2 20.2
Trusted cut-off 20.2 20.2
Noise cut-off 20.1 20.1
Model length: 316
Family (HMM) version: 19
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 are 17 interactions for this family. More...

Cyc-maltodext_C DUF1964 Cyc-maltodext_N DUF1923 DUF1945 Alpha-amylase_N DUF1921 Alpha-amyl_C2 A_amylase_inhib CBM_20 Alpha-amylase_C Alpha-amylase CBM_48 DUF1966 TIG DUF1939 Kunitz_legume

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 Alpha-amylase domain has been found. There are 473 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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