Introduction to Kinases

Introduction to Protein Kinases

Protein Kinases are enzymes that modify the function of other proteins by attaching phosphate groups to them. They are key controllers of most biochemical pathways and important in health and disease. Over 160 protein kinases are associated with human diseases, and several dozen are the targets of drugs in development or already approved.

The kinase reaction

Protein Kinases bind substrate proteins and ATP and transfer a phosphate group from ATP to amino acids with free hydroxyl (-OH) groups (serine, threonine or tyrosine). The products are the phospho-protein and ADP. Most kinases act on serine or threonine, while some are specific to tyrosine, and some act on all three. The phosphate group (PO4-) is negatively charged and changes the substrate protein in different ways – altering activity (including other kinases), the location of the protein, it’s turnover or it’s interactions with other proteins. These changes can be reversed by a separate class of enzymes called phosphatases, that remove the phosphate groups (graphic of kinase/phosphatase reaction).

[Show structures of ser, thr and tyr, and of ATP]

Other kinds of kinases

Histidine Kinases phosphorylate themselves (autophosphorylate) on Histidine, before transferring that phosphate to an Aspartate on a substrate protein (so they are more correctly called Histidine-Aspartate Kinases). Histidine Kinases are common in bacteria (where they are part of the two-component signal transduction mechanisms), plants and lower eukaryotes, but are not found in animals. They are structurally distinct from serine/threonine/tyrosine kinases. Animals do have one class of kinases - mitochondrial pyuvate dehydrogenase kinases - which are structurally similar to histidine kinases, but phosphorylate on serine.

There is some evidence for phosphorylation of other amino acids, though these phoshoamino acids are very labile, making them difficult to work with, and the responsible kinases have not yet been found [add more detail, including histone phosphorylation].

A wide variety of other kinases phosphorylate various small molecules, including those involved in metabolism, such as glycolysis or nucleotide metabolism. These come from a wide variety of different structures, distinct from that of protein kinsaes. One notable exceptions are the phosphatidyl inositol 3' kinases (PI3K). These are structurally related to protein kinases, and a subset of PI3K, known as PIKK, do phosphorylate proteins rather than small molecules.

Special role of phosphotyrosine

Tyrosine phosphoryation has been of particular interest to many biologists, due to its biological roles. Even though only x% of cellular protein is tyrosine phosphorylated (compared with y% on Ser, z% on thr), these sites have strong biological functions, particularly in terms of communication between cells. Most tyrosine phosphorylation is carried out by a distinct group of ePK kinases, called TK (tyrosine kinase), though several ser/thr-looking kinases also have tyrosine kinase abilities (so-called dual-specificity kinases). Most TKs are either receptor tyrosine kinases (RTKs) whose extracellular region senses extracellular signals, or are receptor-associated kinases (is this a term?) that are located near the surface of the cell and interact with RTKs.

Biochemical Functions

Phosphorylation has many effects on proteins. The added charge and bulk of the phosphate can alter the activity of many enzymes (including most kinases), change interactions between proteins, localization or degradation of substrate proteins. Many proteins have multiple phosphorylation sites, which have distinct or even opposing effects in regulating the protein.

Biological Functions

Protein Kinases modify virtually all regulated biochemical pathways and complex behaviors. A few of the more common and more universal roles of protein kinases include:

• Cell cycle control: cyclin dependent kinases (CDKs) control the various checkpoints that control cell cycle.
• Response to extracellular stimuli: Receptor Kinases receive extracellular signals, and intracellular kinase cascades, such as the MAPK cascade, transduce this signal to various cellular components, including transcription.
• DNA damage response: The PIKK family are key mediators that perceive damaged DNA and co-ordinate the repair response.
• Metabolic control

Kinases and Disease

As key regulators, protein kinases have strong effects when misregulated. Over 150 of the 518 human kinases are known to be mutated or misregulated in various diseases, while on the flip side, inhibition of kinases by drugs is a major area of research for disease therapy. Several small molecule drugs and antibodies targetting kinases (mostly receptor tyrosine kinases) are already on the market, mostly as anti-cancer targets, and hundreds of kinase inhibitors are in various stages of development

A list of kinases implicated in disease, and some drug information is available at http://www.cellsignal.com/reference/kinase_disease.asp

Evolution, genomics

Most human protein kinases share a common structural domain, the ePK (eukaryotic protein kinase) domain. Kinases with this domain are almost exclusively eukaryotic, and consitute one of the largest eukaryotic gene families, representing 1-4% of all genes in sequenced genomes. Comparison of the kinomes of several divergent genomes indicates that the most primitive eukaryote had about 35 distinct kinase functions. Humans have 518 protein kinase genes

Classification

Protein kinases have been classified according to their sequence and structure, which frequently, though not always, correlates with their biological functions. There are ten distinct kinase groups, including two polymorphic groups: "Atypical" covers kinases with no sequence similarity to 'typical' (ePK) kinases, though several of them have structural similarity to ePKs. "Other" covers ePKs that don't fall into any of the other 8 groups. Within these groups, kinases are further subdivided into about 100 families and about 150 subfamilies (this classification is expanding as new kinomes are analyzed).

Structure and mechanism (enzymology revisited)

[In-depth analysis of the 3D structure, including secondary structure elements, key residues, faces for regulation, autophosphorylation, differences between groups etc.]

Substrate Recognition

Recognition of correct substrates is complex and still poorly understood. The residues immediately surrounding the site to be phosphorylated show some conservation within distinct kinase groups (e.g. the CMGC kinase usually phosphorylate sites followed by a proline, and most AGC kinases prefer arginine at the -3 and -5 positions). However, these sites on their own give little specificity. Many substrates also have 'docking sites' that bind to the kinase outside of the active site, and many other kinases and substrates are brought together by scaffolding proteins or larger protein complexes, or by clustering in the plasma membrane.

Activation and control mechanisms

Most kinases are themselves controlled by phosphorylation, either by other kinases or by other copies of themselves (autophosphorylation). This allows for complex control of a pathway by means of multiple interacting kinases. The most common form of regulation, found in most kinases, is 'activation loop phosphorylation': these kinases are normally inactive or weakly active, but when a residue on the activation loop, close to the catalytic center, is phosphorylated, the negative phosphate charge neutralizes an inhibitory positive charge in the HRD motif, increasing kinase activity. Other phosphorylation events can inhibit kinase activity, alter its interaction with other proteins, or change its subcellular localization.

Regulatory Subunits

Several kinds of kinases have closely-associated proteins that regulate kinase activity. The best known are the cyclins, which act as regulators of the cell cycle CDK (Cyclin Dependent Kinase) kinases. Others include PKA ((Protein Kinase A), modulated by cAMP, PKG by cGMP, PKA by AKAP proteins, and many more.

Transactivation

This refers to the ability of copies of the same kinase to phosphorylate and activate each other. This is most commonly seen in receptor tyrosine kinases (RTKs), where most active receptors are dimers. Binding of ligand to the extracellular regions of both subunits of the receptor causes them to re-orient such that their kinase domains can phosphorylate each other. Their close proximity means that even 'inactive' forms of the kinase can effectively transphosphorylate. Once activated, their efficiency allows them to phosphorylate additional substrates that are not tethered next to them. Intracellular kinases often form part of larger complexes, and transphosphorylation is also quite common there.