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765  structures 7324  species 0  interactions 59134  sequences 972  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 page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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
SymbolAlpha-amylase_N
PfamPF02903
InterProIPR004185
SCOPe1sma / SUPFAM
Alpha-amylase catalytic domain
PDB 1cyg EBI.jpg
cyclodextrin glucanotransferase (e.c.2.4.1.19) (cgtase)
Identifiers
SymbolAlpha-amylase
PfamPF00128
Pfam clanCL0058
InterProIPR006047
SCOPe1ppi / SUPFAM
CAZyGH13

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 web site,[4][5] and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.[6][7]

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

  1. ^ Henrissat B, Callebaut I, Fabrega S, Lehn P, Mornon JP, Davies G (July 1995). "Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases". Proceedings of the National Academy of Sciences of the United States of America. 92 (15): 7090–4. doi:10.1073/pnas.92.15.7090. PMC 41477. PMID 7624375.
  2. ^ Davies G, Henrissat B (September 1995). "Structures and mechanisms of glycosyl hydrolases". Structure. 3 (9): 853–9. doi:10.1016/S0969-2126(01)00220-9. PMID 8535779.
  3. ^ Henrissat B, Bairoch A (June 1996). "Updating the sequence-based classification of glycosyl hydrolases". The Biochemical Journal. 316 (Pt 2): 695–6. doi:10.1042/bj3160695. PMC 1217404. PMID 8687420.
  4. ^ "Home". CAZy.org. Retrieved 2018-03-06.
  5. ^ Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (January 2014). "The carbohydrate-active enzymes database (CAZy) in 2013". Nucleic Acids Research. 42 (Database issue): D490–5. doi:10.1093/nar/gkt1178. PMC 3965031. PMID 24270786.
  6. ^ "Glycoside Hydrolase Family 13". CAZypedia.org. Retrieved 2018-03-06.
  7. ^ CAZypedia Consortium (December 2018). "Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes" (PDF). Glycobiology. 28 (1): 3–8. doi:10.1093/glycob/cwx089. PMID 29040563.

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) website.

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 ].

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 (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
(18)
Full
(59134)
Representative proteomes UniProt
(251399)
RP15
(7063)
RP35
(26874)
RP55
(57355)
RP75
(98137)
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HTML View             
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
(18)
Full
(59134)
Representative proteomes UniProt
(251399)
RP15
(7063)
RP35
(26874)
RP55
(57355)
RP75
(98137)
Alignment:
Format:
Order:
Sequence:
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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
(18)
Full
(59134)
Representative proteomes UniProt
(251399)
RP15
(7063)
RP35
(26874)
RP55
(57355)
RP75
(98137)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Swissprot
Previous IDs: alpha-amylase;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL , Griffiths-Jones SR
Number in seed: 18
Number in full: 59134
Average length of the domain: 227.50 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 37.26 %

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 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 336
Family (HMM) version: 26
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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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 765 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
A0A0B4KGE4 View 3D Structure Click here
A0A0G2JTB2 View 3D Structure Click here
A0A0P0VPT7 View 3D Structure Click here
A0A0R0I5T6 View 3D Structure Click here
A0A0R0IUQ7 View 3D Structure Click here
A0A0R0KR39 View 3D Structure Click here
A0A140LH76 View 3D Structure Click here
A0A1D6EBQ6 View 3D Structure Click here
A0A1D6EBX4 View 3D Structure Click here
A0A1D6ERN6 View 3D Structure Click here
A0A1D6H9Q8 View 3D Structure Click here
A0A1D6I3N3 View 3D Structure Click here
A0A1D6I698 View 3D Structure Click here
A0A1D6LMR8 View 3D Structure Click here
A0A1D6M3H8 View 3D Structure Click here
A0A1D6NE29 View 3D Structure Click here
A0A1D6PXQ9 View 3D Structure Click here
A0A1D8PP39 View 3D Structure Click here
A0A1D8PQ59 View 3D Structure Click here
A0A1D8PUB9 View 3D Structure Click here
A0A2R8QER5 View 3D Structure Click here
A0A4P1SA55 View 3D Structure Click here
A1Z7E8 View 3D Structure Click here
A1Z7F1 View 3D Structure Click here
A1Z7F2 View 3D Structure Click here
A1Z7F3 View 3D Structure Click here
A1Z992 View 3D Structure Click here
B4FYM6 View 3D Structure Click here
B4G231 View 3D Structure Click here
B9G434 View 3D Structure Click here
C0PGE4 View 3D Structure Click here
C6TCX9 View 3D Structure Click here
D0TZF0 View 3D Structure Click here
D2WL32 View 3D Structure Click here
E9PSQ1 View 3D Structure Click here
E9PV85 View 3D Structure Click here
F1Q7L6 View 3D Structure Click here
F1QEA9 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
I1KPR5 View 3D Structure Click here
I1MXP2 View 3D Structure Click here
I1NAK8 View 3D Structure Click here
K7KF62 View 3D Structure Click here
K7KHN1 View 3D Structure Click here
K7KJ81 View 3D Structure Click here
K7KU93 View 3D Structure Click here
K7L8M7 View 3D Structure Click here
K7MQT1 View 3D Structure Click here
K7MYJ2 View 3D Structure Click here
K7VJE7 View 3D Structure Click here
O04196 View 3D Structure Click here
O13996 View 3D Structure Click here
O14154 View 3D Structure Click here
O18408 View 3D Structure Click here
O23647 View 3D Structure Click here
O42918 View 3D Structure Click here
O42918 View 3D Structure Click here
O45298 View 3D Structure Click here
O53198 View 3D Structure Click here
O74922 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
P07190 View 3D Structure Click here
P07191 View 3D Structure Click here
P07192 View 3D Structure Click here
P07762 View 3D Structure Click here
P08144 View 3D Structure Click here
P08195 View 3D Structure Click here
P0CW40 View 3D Structure Click here
P0CW41 View 3D Structure Click here
P0DTE7 View 3D Structure Click here
P0DTE8 View 3D Structure Click here
P0DUB6 View 3D Structure Click here
P10852 View 3D Structure Click here
P15067 View 3D Structure Click here
P17654 View 3D Structure Click here
P19961 View 3D Structure Click here
P21517 View 3D Structure Click here
P25718 View 3D Structure Click here
P25718 View 3D Structure Click here
P26612 View 3D Structure Click here
P27932 View 3D Structure Click here
P27933 View 3D Structure Click here
P27934 View 3D Structure Click here
P27937 View 3D Structure Click here
P27939 View 3D Structure Click here
P28904 View 3D Structure Click here
P32775 View 3D Structure Click here
P38158 View 3D Structure Click here
P40884 View 3D Structure Click here
P53051 View 3D Structure Click here
P53341 View 3D Structure Click here
P76041 View 3D Structure Click here
P76616 View 3D Structure Click here
P81641 View 3D Structure Click here
P91982 View 3D Structure Click here
P9WN45 View 3D Structure Click here
P9WQ17 View 3D Structure Click here
P9WQ19 View 3D Structure Click here
P9WQ21 View 3D Structure Click here
P9WQ23 View 3D Structure Click here
P9WQ25 View 3D Structure Click here
P9WQ25 View 3D Structure Click here
Q01401 View 3D Structure Click here
Q04446 View 3D Structure Click here
Q07837 View 3D Structure Click here
Q08047 View 3D Structure Click here
Q08295 View 3D Structure Click here
Q09840 View 3D Structure Click here
Q09854 View 3D Structure Click here
Q0D9J1 View 3D Structure Click here
Q10427 View 3D Structure Click here
Q22137 View 3D Structure Click here
Q2FY64 View 3D Structure Click here
Q2G0T9 View 3D Structure Click here
Q41740 View 3D Structure Click here
Q54MA4 View 3D Structure Click here
Q54S16 View 3D Structure Click here
Q54TS5 View 3D Structure Click here
Q555Q9 View 3D Structure Click here
Q5U124 View 3D Structure Click here
Q5VN31 View 3D Structure Click here
Q64319 View 3D Structure Click here
Q6AU80 View 3D Structure Click here
Q6P3H9 View 3D Structure Click here
Q6P5J0 View 3D Structure Click here
Q794F9 View 3D Structure Click here
Q8L735 View 3D Structure Click here
Q8LFG1 View 3D Structure Click here
Q8VZ56 View 3D Structure Click here
Q91WV7 View 3D Structure Click here
Q94A41 View 3D Structure Click here
Q9D6Y9 View 3D Structure Click here
Q9LZS3 View 3D Structure Click here
Q9M0S5 View 3D Structure Click here
Q9P6J3 View 3D Structure Click here
Q9USK8 View 3D Structure Click here
Q9UUL4 View 3D Structure Click here
Q9VKE6 View 3D Structure Click here
Q9XVU3 View 3D Structure Click here
Q9Y719 View 3D Structure Click here
Q9Y7S9 View 3D Structure Click here
X1WDW3 View 3D Structure Click here