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338  structures 5702  species 0  interactions 11900  sequences 84  architectures

Family: Phosphorylase (PF00343)

Summary: Carbohydrate phosphorylase

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Carbohydrate phosphorylase Provide feedback

The members of this family catalyse the formation of glucose 1-phosphate from one of the following polyglucoses; glycogen, starch, glucan or maltodextrin.

Literature references

  1. Leonidas DD, Oikonomakos NG, Papageorgiou AC, Acharya KR, Barford D, Johnson LN; , Protein Sci 1992;1:1112-1122.: Control of phosphorylase b conformation by a modified cofactor: crystallographic studies on R-state glycogen phosphorylase reconstituted with pyridoxal 5'-diphosphate. PUBMED:1304390 EPMC:1304390


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000811

The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([intenz:2.4.1.-]) and related proteins into distinct sequence based families has been described [ PUBMED:9334165 ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.

Glycosyltransferase family 35 CAZY comprises enzymes with only one known activity; glycogen and starch phosphorylase ( EC ).

The main role of glycogen phosphorylase (GPase) is to provide phosphorylated glucose molecules (G-1-P) [ PUBMED:2182117 ]. GPase is a highly regulated allosteric enzyme. The net effect of the regulatory site allows the enzyme to operate at a variety of rates; the enzyme is not simply regulated as "on" or "off", but rather it can be thought of being set to operate at an ideal rate based on changing conditions at in the cell. The most important allosteric effector is the phosphate molecule covalently attached to Ser14. This switches GPase from the b (inactive) state to the a (active) state. Upon phosphorylation, GPase attains about 80% of its Vmax. When the enzyme is not phosphorylated, GPase activity is practically non-existent at low AMP levels.

There is some apparent controversy as to the structure of GPase. All sources agree that the enzyme is multimeric, but there is apparent controversy as to the enzyme being a tetramer or a dimer. Apparently, GPase (in the a form) forms tetramers in the crystal form. The consensus seems to be that `regardless of the a or b form, GPase functions as a dimer in vivo [ PUBMED:2667896 ]. The GPase monomer is best described as consisting of two domains, an N-terminal domain and a C-terminal domain [ PUBMED:8798388 ]. The C-terminal domain is often referred to as the catalytic domain. It consists of a beta-sheet core surrounded by layers of helical segments [ PUBMED:2667896 ]. The vitamin cofactor pyridoxal phosphate (PLP) is covalently attached to the amino acid backbone. The N-terminal domain also consists of a central beta-sheet core and is surrounded by layers of helical segments. The N-terminal domain contains different allosteric effector sites to regulate the enzyme.

Bacterial phosphorylases follow the same catalytic mechanisms as their plant and animal counterparts, but differ considerably in terms of their substrate specificity and regulation. The catalytic domains are highly conserved while the regulatory sites are only poorly conserved. For maltodextrin phosphorylase from Escherichia coli the physiological role of the enzyme in the utilisation of maltidextrins is known in detail; that of all the other bacterial phosphorylases is still unclear. Roles in regulatuon of endogenous glycogen metabolism in periods of starvation, and sporulation, stress response or quick adaptation to changing environments are possible [ PUBMED:10077830 ].

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...

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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
(489)
Full
(11900)
Representative proteomes UniProt
(47638)
RP15
(1800)
RP35
(5940)
RP55
(11415)
RP75
(18097)
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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
(489)
Full
(11900)
Representative proteomes UniProt
(47638)
RP15
(1800)
RP35
(5940)
RP55
(11415)
RP75
(18097)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(489)
Full
(11900)
Representative proteomes UniProt
(47638)
RP15
(1800)
RP35
(5940)
RP55
(11415)
RP75
(18097)
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: Prosite
Previous IDs: phosphorylase;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 489
Number in full: 11900
Average length of the domain: 478.00 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 74.80 %

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 19.4 19.4
Trusted cut-off 19.5 19.4
Noise cut-off 19.3 19.3
Model length: 713
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 Phosphorylase domain has been found. There are 338 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
A0A0P0W399 View 3D Structure Click here
A0A0P0W399 View 3D Structure Click here
A0A1D6L580 View 3D Structure Click here
A0A1D6L580 View 3D Structure Click here
A0A1D6N718 View 3D Structure Click here
A0A1D6N718 View 3D Structure Click here
A0A1D8PQQ3 View 3D Structure Click here
A4IG19 View 3D Structure Click here
E7EXT3 View 3D Structure Click here
E7F2Z5 View 3D Structure Click here
I1KYU6 View 3D Structure Click here
I1LWR4 View 3D Structure Click here
I1N030 View 3D Structure Click here
I1N6A5 View 3D Structure Click here
I1N6A5 View 3D Structure Click here
K7M1G7 View 3D Structure Click here
K7N0Z8 View 3D Structure Click here
K7N0Z8 View 3D Structure Click here
P00490 View 3D Structure Click here
P06737 View 3D Structure Click here
P06738 View 3D Structure Click here
P09811 View 3D Structure Click here
P09812 View 3D Structure Click here
P0AC86 View 3D Structure Click here
P11216 View 3D Structure Click here
P11217 View 3D Structure Click here
P34114 View 3D Structure Click here
P53534 View 3D Structure Click here
P9WMW1 View 3D Structure Click here
P9WMW1 View 3D Structure Click here
Q00766 View 3D Structure Click here
Q503C7 View 3D Structure Click here
Q59025 View 3D Structure Click here
Q8CI94 View 3D Structure Click here
Q8LQ33 View 3D Structure Click here
Q9ET01 View 3D Structure Click here
Q9LIB2 View 3D Structure Click here
Q9N5U1 View 3D Structure Click here
Q9SD76 View 3D Structure Click here
Q9WUB3 View 3D Structure Click here
Q9XTL9 View 3D Structure Click here