The hundreds of unique protein kinases found in eukaryotic cells are organized into complex networks of signaling pathways. These pathways serve to coordinate the activities of the cell, control the cell cycle, and transport messages into the cell from the cell's surroundings. The cell must be able to integrate as well as amplify a good number of the associated extracellular signals in order to function properly. Certain protein kinases, along with other signaling proteins, perform the function of input-output devices, also known as "microprocessors," during the integration process.

These signal-processing proteins get a substantial portion of their input from the control that protein kinases and protein phosphatases exert over the phosphates that are either added to or removed from them, respectively. This control is carried out by protein kinases and protein phosphatases.

Protein kinases that belong to the Src family are responsible for these types of activities. The Src protein was the first tyrosine kinase to be discovered. Its name, which is pronounced "sarc," comes from the sarcoma tumor subtype that can develop as a result of its dysregulation. This protein was the first tyrosine kinase to be discovered. It is now widely accepted that it is a member of a subfamily of nine protein kinases that are exclusive to multicellular animals and share a great deal of homology with one another. The kinase is anchored at the cytoplasmic face of the plasma membrane by a short N-terminal region that can be found in the Src protein as well as related proteins. This region forms a covalent bond with a very hydrophobic fatty acid. Along the linear sequence of amino acids comes the kinase catalytic domain, which is then followed by two peptide-binding domains: a Src homology 3 (SH3) domain and an SH2 domain.

The SH2 domain of these kinases is generally connected to a phosphorylated tyrosine near the C-terminus, and the SH3 domain is connected to an internal peptide in a manner that distorts the active site of the enzyme and helps to render it inactive. Both of these connections are made in a manner that allows the SH2 domain to remain connected to the SH3 domain.

To activate the kinase, it is necessary to remove the phosphate group from the C-terminus and for a specific activating protein to attach to the SH3 domain. These are the bare minimum requirements. In this approach, the activation of the Src kinase signifies the culmination of a particular series of separate upstream events. The Src family of protein kinases contributes to the complex network of information-processing processes that enable the cell to compute appropriate responses to a wide variety of challenging circumstances. These protein kinases act as specific signal integrators, and their involvement in these processes is essential.

In the previous lesson, we went through how a cell can control the activity of a protein by either adding to or removing from the protein phosphate groups. In the example that was just presented, a kinase is responsible for moving a phosphate from a molecule of ATP to the side chain of amino acids on a target protein. Eukaryotic cells have multiple mechanisms at their disposal for controlling protein activity. One of these mechanisms is the addition and removal of phosphate. In this particular instance, the phosphate is not directly linked to the protein; rather, it is a component of the guanine nucleotide GTP, which forms an extremely strong bond with a group of proteins known as GTP-binding proteins. In other words, the phosphate is not directly linked to the protein; rather, it is a component of GTP. The majority of the time, proteins that are regulated in this manner have GTP coupled to them and are in their active conformations.

A phosphate group is lost and the protein becomes inactive when it is bound to GDP because this process, which is catalyzed by the protein itself, hydrolyzes bound GTP into GDP. This process is catalyzed by the protein. To put it another way, the ability of GTP-binding proteins to serve as on-off switches is controlled by whether or not an additional phosphate is present on a GDP molecule that is bound.

GTP-binding proteins are a broad class of proteins that all have variants on the same GTP-binding globular domain. These proteins are also known as GTPases due to the fact that they catalyze the hydrolysis of GTP. This domain goes through a conformational change that renders the protein inactive when a tightly bound GTP is degraded by the GTP-binding protein to produce GDP. The prototypical member of this family is called Ras, and it is a monomeric GTPase that has a three-dimensional structure.

The role that Ras plays in cell signaling cannot be overstated. When it is coupled to GTP, it becomes functional and kicks off a chain reaction of protein phosphorylations throughout the cell. On the other hand, the protein is GDP-bound and inactive the vast majority of the time. It enters an active state when, in response to external cues such as growth factors that adhere to plasma membrane receptors, it trades its GDP for a GTP molecule and therefore becomes activated.

In the same way that protein kinases and protein phosphatases can activate or deactivate phosphorylated proteins, regulatory proteins can determine whether GTP or GDP is bound to GTP-binding proteins. Ras can be rendered inactive by a protein called a GTPase-activating protein, or GAP. This protein binds to the Ras protein and induces Ras to hydrolyze the GTP molecule that it is attached to, producing GDP, which continues to be tightly bound, and inorganic phosphate (Pi), which is swiftly released. The inactive state of the Ras protein, in which it is linked to GDP, is maintained up until the point at which it is brought into contact with a guanine nucleotide exchange factor (GEF). Once the GEF has established its connection to Ras, Ras will unbind its GDP.

The GEF is responsible for the indirect activation of Ras. This is accomplished by the GEF replacing the phosphate that was removed during GTP hydrolysis. This allows for the unoccupied nucleotide-binding site to be immediately replaced by a GTP molecule (GTP is available in cells in significant excess over GDP). Therefore, in some respects, the roles of a protein phosphatase and a protein kinase are comparable to those of a GAP and a GEF, respectively.

There is a certain family of very small proteins that may be found in cells. The members of this family are covalently attached to a large number of other proteins, which allows them to affect the activity or fate of the second protein. In each instance, the amino group of a lysine side chain on a "target" protein forms an isopeptide bond with the carboxyl terminus of the small protein. This results in the formation of an isopeptide bond. Ubiquitin was the first protein of this kind to be found, and it is still the one that is utilized the most. Ubiquitin is the most common protein that has been discovered and utilized. There are many different ways that ubiquitin can form covalent bonds with target proteins; each of these ways has its own unique set of effects on the cell. After the first ubiquitin molecule has attached itself to the target, each subsequent ubiquitin molecule will attach itself to Lys48 of the ubiquitin that came before it. This will result in the formation of a chain of Lys48-linked ubiquitins that are attached to a single lysine side chain of the target protein. This particular variety of polyubiquitin is responsible for transporting the target protein to the inside of the proteasome, where it is subsequently broken down into peptide fragments. In other instances, only a single molecule of ubiquitin is linked to a protein. In addition, the target proteins for several of these modifications each receive their own polyubiquitin chain. The targeted protein is subject to a variety of different functional consequences as a result of these alterations.

Similar structures are produced when a different ubiquitin, such as SUMO (small ubiquitin-related modifier), is covalently joined to a lysine side chain of a target protein. SUMO is an acronym that stands for small ubiquitin-related modifier. Naturally, each and every one of these shifts can be rolled back. Cells contain sets of enzymes that can ubiquitylate and deubiquitylate proteins, as well as sumoylate and desumoylate proteins, in order to regulate the formation of covalent adducts. The functions performed by these enzymes are analogous to those performed by protein phosphatases and kinases, which respectively add and remove phosphates from the side chains of proteins.