Summary: Carbohydrate phosphorylase
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.
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
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 (EC) 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'.
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].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||phosphorylase activity (GO:0004645)|
|Biological process||carbohydrate metabolic process (GO:0005975)|
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This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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This is the GT-B clan that contains diverse glycosyltransferases that possess a Rossmann like fold .
The clan contains the following 35 members:Alg14 Capsule_synth DUF1205 DUF1972 DUF3492 DUF354 Epimerase_2 Glyco_tran_28_C Glyco_trans_1_2 Glyco_trans_1_3 Glyco_trans_1_4 Glyco_trans_4_2 Glyco_trans_4_3 Glyco_trans_4_4 Glyco_transf_20 Glyco_transf_28 Glyco_transf_4 Glyco_transf_41 Glyco_transf_5 Glyco_transf_56 Glyco_transf_9 Glyco_transf_90 Glycogen_syn Glycos_transf_1 Glycos_transf_N Glyphos_transf LpxB MGDG_synth Mito_fiss_Elm1 Phosphorylase PIGA PS_pyruv_trans SUA5 Sucrose_synth UDPGT
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||9|
|Number in full:||4954|
|Average length of the domain:||590.10 aa|
|Average identity of full alignment:||40 %|
|Average coverage of the sequence by the domain:||79.46 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 252 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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