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224  structures 5935  species 0  interactions 10432  sequences 158  architectures

Family: Alpha-amylase_C (PF02806)

Summary: Alpha amylase, C-terminal all-beta domain

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

Alpha-Amylase Edit Wikipedia article

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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, C-terminal all-beta 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 IPR006048

Alpha-amylase is classified as family 13 of the glycosyl hydrolases and is present in archaea, bacteria, plants and animals. Alpha-amylase is an essential enzyme in alpha-glucan metabolism, acting to catalyse the hydrolysis of alpha-1,4-glucosidic bonds of glycogen, starch and related polysaccharides. Although all alpha-amylases possess the same catalytic function, they can vary with respect to sequence. In general, they are composed of three domains: a TIM barrel containing the active site residues and chloride ion-binding site (domain A), a long loop region inserted between the third beta strand and the alpha-helix of domain A that contains calcium-binding site(s) (domain B), and a C-terminal beta-sheet domain that appears to show some variability in sequence and length between amylases (domain C) [ PUBMED:11141191 ]. Amylases have at least one conserved calcium-binding site, as calcium is essential for the stability of the enzyme. The chloride-binding functions to activate the enzyme, which acts by a two-step mechanism involving a catalytic nucleophile base (usually an Asp) and a catalytic proton donor (usually a Glu) that are responsible for the formation of the beta-linked glycosyl-enzyme intermediate.

This entry represents the all-beta C-terminal domain that is found in members of the glycosyl hydrolase 13 family, such as alpha-amylases and 1,4-alpha-glucan branching enzyme. This domain forms a Greek key beta-barrel fold in these enzymes [ PUBMED:7877175 ].

Branching enzyme catalyses the formation of alpha-1,6 branch points in either glycogen or starch. It has an important role in the determination of the structure of starch in plants and of glycogen in animals and bacteria [ PUBMED:12196524 ].

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

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(242)
Full
(10432)
Representative proteomes UniProt
(40060)
RP15
(1463)
RP35
(4927)
RP55
(10047)
RP75
(16414)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(242)
Full
(10432)
Representative proteomes UniProt
(40060)
RP15
(1463)
RP35
(4927)
RP55
(10047)
RP75
(16414)
Alignment:
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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
(242)
Full
(10432)
Representative proteomes UniProt
(40060)
RP15
(1463)
RP35
(4927)
RP55
(10047)
RP75
(16414)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: ref [2]
Previous IDs: alpha-amylase_C;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL , Griffiths-Jones SR
Number in seed: 242
Number in full: 10432
Average length of the domain: 93.80 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 13.53 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 17.0
Trusted cut-off 21.2 17.0
Noise cut-off 21.1 16.9
Model length: 96
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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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_C domain has been found. There are 224 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JTB2 View 3D Structure Click here
A0A0N7KFE7 View 3D Structure Click here
A0A0R0JAD6 View 3D Structure Click here
A0A140LH76 View 3D Structure Click here
A0A1D6EBQ6 View 3D Structure Click here
A0A1D6H9Q8 View 3D Structure Click here
A0A1D8PQ59 View 3D Structure Click here
A1Z992 View 3D Structure Click here
D2WL32 View 3D Structure Click here
E9PSQ1 View 3D Structure Click here
F1QTT5 View 3D Structure Click here
F1RD28 View 3D Structure Click here
F8W5I0 View 3D Structure Click here
I1JPY7 View 3D Structure Click here
I1NAK8 View 3D Structure Click here
K7KHN1 View 3D Structure Click here
K7MQT1 View 3D Structure Click here
K7VJE7 View 3D Structure Click here
O18408 View 3D Structure Click here
O23647 View 3D Structure Click here
P00687 View 3D Structure Click here
P00688 View 3D Structure Click here
P00689 View 3D Structure Click here
P04746 View 3D Structure Click here
P07762 View 3D Structure Click here
P08144 View 3D Structure Click here
P0DTE7 View 3D Structure Click here
P0DTE8 View 3D Structure Click here
P0DUB6 View 3D Structure Click here
P19961 View 3D Structure Click here
P26612 View 3D Structure Click here
P32775 View 3D Structure Click here
P81641 View 3D Structure Click here
P9WN45 View 3D Structure Click here
Q01401 View 3D Structure Click here
Q04446 View 3D Structure Click here
Q08047 View 3D Structure Click here
Q22137 View 3D Structure Click here
Q41740 View 3D Structure Click here
Q555Q9 View 3D Structure Click here
Q5VN31 View 3D Structure Click here
Q6P5J0 View 3D Structure Click here
Q9D6Y9 View 3D Structure Click here
Q9LZS3 View 3D Structure Click here