Summary

Alpha amylase, catalytic domain

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

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
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

InterPro entry IPR006047

O-Glycosyl hydrolases 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, PUBMED:. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site PUBMED:. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in clans.

Enzymes containing this domain, such as alpha-amylase, belong to family 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 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:.

Clan

This family is a member of clan Glyco_hydro_tim (CL0058), which contains the following 30 members:

Alpha-amylase Alpha_L_fucos Cellulase DUF187 DUF297 Glyco_hydro_1 Glyco_hydro_10 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_53 Glyco_hydro_56 Glyco_hydro_59 Glyco_hydro_70 Glyco_hydro_72 Glyco_hydro_77 Glyco_hydro_97 Glyco_hydro_cc Melibiase Raffinose_syn

Gene Ontology

Molecular function	cation binding (GO:0043169)
Molecular function	catalytic activity (GO:0003824)
Biological process	carbohydrate metabolic process (GO:0005975)

Internal database links

SCOOP:

Cellulase Glyco_hydro_70 NosD TSP_3 CBM_48 DUF871

External database links

CAZY:	GH_13
HOMSTRAD:	ghf13
PANDIT:	PF00128
PRINTS:	PR00110
SCOP:	1ppi
SYSTERS:	Alpha-amylase

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

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Alignment:	Seed (31) Full (10389) NCBI (12620) Metagenomics (3054)
Viewer:

Formatting options

Alignment:	Seed (31) Full (10389)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

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

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (31) Full (10389) NCBI (12620) Metagenomics (3054)
Full length sequences	Full-sequences (10389)

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 HMMER2.

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. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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:

Swissprot

Previous IDs:

alpha-amylase;

Type:

Domain

Author:

Sonnhammer ELL, Griffiths-Jones SR

Number in seed:

31

Number in full:

10389

Average length of the domain:

262.20 aa

Average identity of full alignment:

19 %

Average coverage of the sequence by the domain:

39.89 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 9421015 -E 1000 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:

17

Download:

download the raw HMM for this family

Species distribution

Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Interactions

There are 17 interactions for this family. More...

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

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.

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Family: Alpha-amylase (PF00128)

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