Detailed Report on Pyruvate Kinase: Structure, Function, Regulation

This report provides a detailed analysis of Pyruvate Kinase (protein code 3EOW) from Leishmania Mexicana (LmPYK), an enzyme crucial in the final stage of glycolysis. The report elucidates the enzyme's function in catalyzing the transfer of a phosphate group from phosphoenolpyruvate (PEP) to adenosine diphosphate (ADP), yielding ATP and pyruvate. It discusses the protein's various binding sites, regulation via fructose 2,6-bisphosphate, and its existence in four tissue-specific isozymes with distinct kinetic properties. The analysis covers the protein's structure, including its all-beta protein class, PK beta-barrel domain, and tetrameric quaternary structure with metal-binding sites for Mg2+ and K+ ligands. A comparison with human hemoglobin highlights both similarities and differences in subunit structure and ligand binding. The report further discusses the temperature-dependent conformational states and immunological cross-reactivity with heat shock proteins, offering a comprehensive overview of Pyruvate Kinase's structure, function, and regulation.

Protein Data Bank

Protein code: 3EOW
The given protein is Pyruvate Kinase from leishmania Mexicana (LmPYK).
The protein is contained in end stage of glycolysis which catalyzes the shift of phosphate
group from PEP (PhosPhenolpyruvate) to ADP (Adenosine Diphosphate) that yields one
molecule of ATP (Allostric regulation of pyruvate) and one of pyruvate (Grace and et.al.,
2019).
The protein have various binding sites and it is operated through fructose 2, 6-bisphosphate
as well as activated through the effector in a intractable way. Pyruvate Kinase is a
phosphatase protein which is considered as naming error. The protein exists in 4 different
tissue-specific iszoymes in animas. Every tissue specific isozyme consist of a certain kinetic
properties which are needed to accommodate the differences in metabolic requirement of
distinct tissues.
Figure 1An overview of structure, function, and regulation of pyruvate kinases. 2019
The Pyruvate Kinase is found in Homo sapiens. It is associated with all beta
protein class as well as also have the PK beta-barrel domain which is like a fold. Pyruvate
Kinase belongs to PK beta-barrel domain family as well to PK beta-barrel domain
superfamily. Pyruvate Kinase can be transformed into all beta proteins. But its structure
involves both beta sheets and alpha helices. Pyruvate Kinase have four domains in human
body when it is observed in the quaternary structure (Lewandowski and et.al., 2020).
Therefore, Pyruvate Kinase enzyme is tetameric with metal binding on every domain for

Mg2+ and K+ ligands to bind with. The four kinds of classification of tissue certain isozymes
in Pyruvate Kinase are as follows:
L (Liver)
M1 (Muscle, brain and heart)
R (Red Blood Cells)
M2 (early fetal tissue).
The Cytosolic Pyks composes of 480-530 of amino acids and the apicoplast-specific and
plastid PyKs carry additional sequence of N-terminal.
Figure 2Probe Reports from the NIH Molecular Libraries Program: Pyruvate Kinase
Pyruvate Kinase transfers the final reaction of Glycolysis. It is tetrameric
protein which is associated to identical subunits that are arranged in a dimer-of-dimer
configuration situation. Every monomer of it contains an active site. Every monomer is
composed with three main domains such as designed A, B, C as well as a small N-terminal.
The active site is situated at end of barrel which in a cleft between A domain and B domain
(Zahra and et.al., 2020). Here the A domain is largest domain in all domains. Domain B is
mobile which closes on active site on Mg2+ -ADP binding of substrate complex. The C
Domain on the hand is situated on the contrary site of domain A. This involves the fructose-1,
6-bisphosphate (FBP) which is a binding pocket existing in PKM2, PKR and PKL isoforms.

Most of the Pyks are homo-tetrameric proteib. But some other oligomeric forms have also
been discovered. As there protein folds into three domains such as A, B and C, as well as an
additional N terminal which is α-helical domain also resided the of ~17which is called as N-
domain. Also there are other extra C-terminal domains of bacteria like Cyanobackteris,
Staphylococcus and Bacillus species. A domain is largest which composes of two segments
residues 187-356 and 18-88. The domain B residues between 89-186 and have a mixed up β-
barrel topology (Grace and et.al., 2018). It contains one or two short α-helical. It is also
referred sometimes as the lid domain as it binds the substrate through undergoing a curve
motion that as a result, goes on in active site closure.
When Pyruvate Kinase is compared with the human haemoglobin, various similar
features and differences could be analysed. The difference can be analysed from the ligands
as Pyruvate Kinase have Mg2+ and K+ ligands while Haemoglobin contains HEM and PO4
ligands in it. However, there are some similarities between the both. As per PDB website the
haemoglobin have 4 subunits and every unit contains a heam group as well as a polypeptide
chain. In adult human body there are alpha and beta polypepetides chains which gives a
quaternary structure to haemoglobin. Thus the structures of haemoglobin and Pyruvate
Kinase are similar. Also the Pyruvate Kinase is also involves four subunits in its structure.
Many Pyruvate Kinase can exists in 2 temperature-dependent conformation states (Grace,
Mark Layton and Barcellini, 2019). The heat shock protein of molecular mass and Pyruvate
Kinase are cross-reaching immunologically. The heat shocked Xenopus embryos enhances
the synthesis of Pyruvate Kinase isoform. The thermal denaturation states that the isoform
increases thermal stability.

REFERENCES:
Books and journals:
Grace, R.F. and et.al., 2018. Clinical spectrum of pyruvate kinase deficiency: data from the
Pyruvate Kinase Deficiency Natural History Study. Blood, The Journal of the
American Society of Hematology. 131(20). pp.2183-2192.
Grace, R.F. and et.al., 2019. Safety and efficacy of mitapivat in pyruvate kinase
deficiency. New England Journal of Medicine. 381(10). pp.933-944.
Grace, R.F., Mark Layton, D. and Barcellini, W., 2019. How we manage patients with
pyruvate kinase deficiency. British journal of haematology. 184(5). pp.721-734.
Lewandowski, S.L. and et.al., 2020. Pyruvate kinase controls signal strength in the insulin
secretory pathway. Cell metabolism. 32(5). pp.736-750.
Zahra, K. and et.al., 2020. Pyruvate kinase M2 and cancer: the role of PKM2 in promoting
tumorigenesis. Frontiers in oncology. 10. P.159.
Online references:
An overview of structure, function, and regulation of pyruvate kinases. 2019. [Online].
Available through: < https://onlinelibrary.wiley.com/doi/full/10.1002/pro.3691/ >
Probe Reports from the NIH Molecular Libraries Program. [Online]. Available through: <
https://www.ncbi.nlm.nih.gov/books/NBK148850/figure/ml285.f6/ >