Summary: Pyruvate kinase, barrel domain
Pyruvate kinase, barrel domain Provide feedback
This domain of the is actually a small beta-barrel domain nested within a larger TIM barrel. The active site is found in a cleft between the two domains.
Larsen TM, Benning MM, Wesenberg GE, Rayment I, Reed GH; , Arch Biochem Biophys 1997;345:199-206.: Ligand-induced domain movement in pyruvate kinase: structure of the enzyme from rabbit muscle with Mg2+, K+, and L-phospholactate at 2.7 A resolution. PUBMED:9308890 EPMC:9308890
Internal database links
|SCOOP:||IMPDH HpcH_HpaI DUF1273 DUF4253|
|Similarity to PfamA using HHSearch:||HpcH_HpaI|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015793
The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues.
PK helps control the rate of glycolysis, along with phosphofructokinase (INTERPRO) and hexokinase (INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions [PUBMED:12798932]. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver.
The structure of several pyruvate kinases from various organisms have been determined [PUBMED:11960989, PUBMED:10751408]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain.
This entry represents the two barrel domains, the beta/alpha-barrel, and the beta-barrel inserted within it.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||potassium ion binding (GO:0030955)|
|magnesium ion binding (GO:0000287)|
|pyruvate kinase activity (GO:0004743)|
|Biological process||glycolytic process (GO:0006096)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This superfamily consists of a number of TIM barrel domains found in enzymes such as pyruvate kinase, malate synthase and citrate lyase.
The clan contains the following 11 members:C-C_Bond_Lyase HpcH_HpaI ICL Malate_synthase Pantoate_transf PEP-utilizers_C PEP_hydrolase PEP_mutase PEPcase PEPcase_2 PK
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Author:||Finn RD, Griffiths-Jones SR|
|Number in seed:||11|
|Number in full:||3454|
|Average length of the domain:||316.10 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||66.46 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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There are 5 interactions for this family. More...
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 PK domain has been found. There are 325 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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