Protein kinase

A protein kinase is an enzyme that can transfer a phosphate group from a donor molecule (usually ATP) to an amino acid residue of a protein. Enzymes that transfer phosphate groups are known as kinases. The protein kinase mechanism is used in signal transduction for the regulation of enzymes: phosphorylation can activate (or inhibit) the activity of an enzyme. Although most protein kinases are specialized for a single kind of amino acid residue, some exhibit dual kinase activity (they can phosphorylate two different kinds of amino acid).

Protein kinases can be regulated by:

• Activator proteins
• Inhibitor proteins
  • Pseudosubstrates
  • Autoinhibition (a part of the protein kinase mimics a pseudosubstrate)
• Ligand binding to regulatory subunits
• Cofactors / second messenger
• Phosphorylation in the active center (intrasterical regulation) by:
  • other protein kinases (trans-phosphorylation)
  • itself (cis-phosphorylation/autophosphorylation)
• Location within the cell

Serine/threonine-specific protein kinases

Serine/threonine protein kinases phosphorylate the OH group of serine or threonine (which have similar sidechains). These protein kinases can be regulated by:

• cAMP/cGMP
• Diacylglycerol
• Ca²⁺/calmodulin

These kinases are not specific to a similar consensus sequence; that is, there is no common "target sequence" to be phosphorylated. Since the substrate to be phosphorylated aligns with the kinase by several key amino acids (usually through hydrophopic forces and ionic bonds), a kinase is usually specific, not to a single substrate, but to a whole "substrate family" having common properties. The kinases are usually inactivated by a pseudosubstrate that binds to the kinase like a real substrate but lacks the amino acid to be phosphorylated. Its removal activates the kinase.

The catalytic domain of these kinases is highly conserved.

Phosphorylase kinase

Phosphorylase kinase was the first Ser/Thr protein kinase to be discovered (in 1959 by Krebs et al.).

Protein kinase A

Protein kinase A consists of two domains, a small domain with several β sheet structures and a larger domain containing several α helices. The binding sites for substrate and ATP are located in the catalytic cleft between the domains (or lobes). When ATP and substrate bind, the two lobes rotate so that the terminal phosphate group of the ATP and the target amino acid of the substrate move into the correct positions for the catalytic reaction to take place.

Regulation

Protein kinase A has several functions in the cell, including regulation of glycogen, sugar, and lipid metabolism. It is controlled by cAMP: in the absence of cAMP, the kinase is a tetramer of two regulatory and two catalytic subunits (R₂C₂), with the regulatory subunits blocking the catalytic center of the catalytic subunits. Binding of cAMP to the regulatory subunit leads to dissociation of active RC dimers. Also, the catalytic subunit itself can be regulated by phosphorylation.

Downregulation of protein kinase A occurs by a feedback mechanism: one of the substrates that is activated by the kinase is a phosphodiestrase, which converts cAMP to AMP, thus reducing the amount of cAMP that can activate protein kinase A.

Protein kinase C

Protein kinase C is actually a family of protein kinases that require Ca²⁺, diacylglycerol, and a phospholipid such as phosphatidylcholine for activation. Thus, protein kinase C is activated through the same signal transduction pathway as phospholipase C. At least twelve members of the proteine kinase C family have been identified in mammals, due to their high sequence homology. The protein kinase C usually means the protein kinase Cα enzyme.

Structure and regulation

Protein kinase C enzymes consist of an N-terminal regulatory domain and a C-terminal catalytic domain. The kinases are inactive in the absence of activating agents, due to autoinhibition of the regulatory domain. They can be activated tumor promotors such as tetradecanoyl-phorbol-acetate (TPA) or by the cofactors Ca²⁺, diacylglycerol, and a phospholipid. The common linear structure of protein kinase C enzymes is:

N - pseudosubstrate - TPA-binding - (Ca²⁺-binding) - ATP-binding - substrate-binding - C

Upon activation, protein kinase C enzymes are translocated to the plasma membrane by RACK proteins (membrane-bound receptor for activated protein kinase C proteins). The protein kinase C enzymes are known for their long-term activation: they remain activated after the original activation signal or the Ca²⁺-wave is gone. This is presumably achieved by the production of diacylglycerol from phosphatidylcholine by a phospholipase; fatty acids may also play a role in long-term activation.

Function

The consensus sequence of protein kinase C enzymes is similar to that of protein kinase A, since it contains basic amino acids close to the Ser/Thr to be phosphorylated. Their substrates are MARCKS proteins, MAP kinase, transcription factor inhibitor I_XB, the vitamin D₃ receptor VDR, Raf kinase, calpain, and the EGF receptor.

Ca²⁺/calmodulin-dependent protein kinases

Also called CaM kinases, these kinases are primarily regulated by the Ca²⁺/calmodulin complex. These kinases show a memory effect on activation. Two types of CaM kinases are:

• Specialized CaM kinases. An example is the myosin light chain kinase (MLCK) that phosphorylates myosin, causing muscles to contract.
• Multifunctional CaM kinases. Also collectively called CaM kinase II, which play a role in many processes, such as neurotransmitter secretion, transcription factor regulation, and glycogen metabolism.

Structure and autoregulation

The CaM kinases consist of an N-terminal catalytic domain, a regulatory domain, and an associative domain. In the absence of Ca²⁺/calmodulin, the catalytic domain is autoinhibited by the regulatory domain, which contains a pseudosubstrate sequence. Several CaM kinases aggregate into a homooligomer or heterooligomer. Upon activation by Ca²⁺/calmodulin, the activated CaM kinases autophosphorylate each other in an intermolecular reaction. This has two effects:

1. An increase in affinity for the calmodulin complex, prolonging the time the kinase is active.
2. Continued activation of the phosphorylated kinase complex even after the calmodulin complex has dissociated from the kinase complex, which prolongs the active state even more.

MAP kinases

Mos/Raf kinases

Tyrosine-specific protein kinases

Tyrosine-specific protein kinases are, like serine/threonine-specific kinases, used in signal transduction. They act primarily as growth factor receptors, for example, the platelet derived growth factor, epidermal growth factor, transforming growth factor, insulin and insulin-like growth factor, interleukins, and tumor necrosis factor.

Receptor tyrosine kinases

These kinases consist of a transmembrane receptor with a tyrosine kinase domain protruding into the cytoplasm. They play an important role in regulating cell division, cellular differentiation, and morphogenesis. More than 50 known receptor tyrosine kinases are known in mammals.

Structure

The extracellular domain serves as the ligand receptor. It can be a separate unit that is attached to the rest of the receptor by a disulfide bond. The same mechanism can be used to bind two receptors together to form a homo- or heterodimer. The transmembrane element is a single α helix. The intracellular or cytoplasmic domain is responsible for the (highly conserved) kinase activity, as well as several regulatory functions.

Regulation

Ligand binding causes two reactions:

1. Dimerization of two monomeric receptor kinases or stabilization of a loose dimer. Many ligands of receptor tyrosine kinases are multivalent. Some tyrosine receptor kinases (e.g., the platelet derived growth factor receptor) can form heterodimers with other similar but not identical kinases of the same subfamily, allowing a highly varied response to the extracellular signal.
2. Trans-autophosphorylation (phosphorylation by the other kinase in the dimer) of the kinase.

The autophosphorylation causes the two subdomains of the intrinsic kinase to shift, opening the kinase domain for ATP binding. In the inactive form, the kinase subdomains are aligned so that ATP cannot reach the catalytic center of the kinase. When several amino acids suitable for phosphorylation are present in the kinase domain (e.g., the insulin-like growth factor receptor), the activity of the kinase can increase with the number of phosphorylated amino acids; in this case, the first phosphorylation is said to be a cis-autophosphorylation, switching the kinase from "off" to "standby".

Signal transduction

The active tyrosine kinase phosphorylates specific target proteins, which are often enzymes themselves. An important target is the ras protein signal-transduction chain.

Histidine-specific protein kinases

Aspartic acid/glutamic acid-specific protein kinases