Covalent modification by phosphorylation

Many proteins can be phosphorylated at multiple sites or are subject to regulation both by phosphorylation-dephosphorylation and by the binding of allosteric ligands. Phosphorylation-dephosphorylation at any one site can be catalyzed by multiple protein kinases or protein phosphatases. Many protein kinases and most protein phosphatases act on more than one protein and are themselves interconverted between active and inactive forms by the binding of second messengers or by covalent modification by phosphorylation-dephosphorylation. 

Covalent modification by phosphorylation and dephosphorylation of hydroxyl groups on amino acid side chains. 

Approximately one-third of cellular proteins contain phosphate and are subject to covalent modification by phosphorylation and dephosphorylation reactions. This reversible phosphorylation of proteins causes conformational changes in the protein that dramatically alters their properties, e.g. from an active to an inactive enzyme, or vice versa. The sites of protein phosphorylation are those amino acid residues that contain hydroxyl groups, most commonly serine but also tyrosine and threonine (Fig. 27.2) (Chapter 31). Phosphorylation uses protein kinase and dephosphorylation uses protein phosphatase. The importance of reversible protein phosphorylation to the living cell is emphasised by the fact that protein kinases and protein phosphatases comprise approximately 5% of the proteins encoded by the human genome. Current research is discovering abnormalities of protein phosphorylation that are associated with diseases, notably type 2 diabetes meUitus (T2DM) and cancer. In the future, the discovery of drugs that modify protein phosphorylation/dephosphorylation promises new therapies for the treatment of these diseases. 

The serine residue of isocitrate dehydrogenase that is phos-phorylated by protein kinase lies within the active site of the enzyme. This situation contrasts with most other examples of covalent modification by protein phosphorylation, where the phosphorylation occurs at a site remote from the active site. What direct effect do you think such active-site phosphorylation might have on the catalytic activity of isocitrate dehydrogenase (See Barford, D., 1991. Molecular mechanisms for the control of enzymic activity by protein phosphorylation. Bioehimiea et Biophysiea Acta 1133 55-62.)... 

Ghanges in the availability of substrates are responsible for most changes in metabolism either directly or indirectly acting via changes in hormone secretion. Three mechanisms are responsible for regulating the activity of enzymes in carbohydrate metabolism (1) changes in the rate of enzyme synthesis, (2) covalent modification by reversible phosphorylation, and (3) allosteric effects. 

Acetyl-CoA carboxylase activity can be altered by interaction with citrate and other tricarboxylic acids. Much attention has been paid to hepatocyte systems where compounds such as glucagon or dibutyryl cyclic AMP lower cytosolic citrate levels which cause a lowered acetyl-CoA carboxylase activity (Lane et al, 1979). The latter is also inhibited by raised fatty acyl-CoA concentrations which cause depolymerization of the mammalian carboxylase. Information is available concerning inhibitor specificity and interactions with other subcellular compounds (cf. Wakil et al, 1983). The mammalian acetyl-CoA carboxylase has also been reported to undergo covalent modification through phosphorylation/ dephosphorylation. Such regulation may involve the simultaneous presence of Co A (Yeh et aL, 1981). Various kinase and phosphatase enzymes which may be important in the modification of the mammalian acetyl-CoA carboxylase have been purified (cf. Wakil etal., 1983). 

FIGURE 15.2 Enzymes regulated by covalent modification are called interconvertible enzymes. The enzymes protein kinase and protein phosphatase, in the example shown here) catalyzing the conversion of the interconvertible enzyme between its two forms are called converter enzymes. In this example, the free enzyme form is catalytically active, whereas the phosphoryl-enzyme form represents an inactive state. The —OH on the interconvertible enzyme represents an —OH group on a specific amino acid side chain in the protein (for example, a particular Ser residue) capable of accepting the phosphoryl group. 

Pyruvate kinase possesses allosteric sites for numerous effectors. It is activated by AMP and fructose-1,6-bisphosphate and inhibited by ATP, acetyl-CoA, and alanine. (Note that alanine is the a-amino acid counterpart of the a-keto acid, pyruvate.) Furthermore, liver pyruvate kinase is regulated by covalent modification. Flormones such as glucagon activate a cAMP-dependent protein kinase, which transfers a phosphoryl group from ATP to the enzyme. The phos-phorylated form of pyruvate kinase is more strongly inhibited by ATP and alanine and has a higher for PEP, so that, in the presence of physiological levels of PEP, the enzyme is inactive. Then PEP is used as a substrate for glucose synthesis in the pathway (to be described in Chapter 23), instead... 

In mammalian cells, the two most common forms of covalent modification are partial proteolysis and ph osphorylation. Because cells lack the ability to reunite the two portions of a protein produced by hydrolysis of a peptide bond, proteolysis constitutes an irreversible modification. By contrast, phosphorylation is a reversible modification process. The phosphorylation of proteins on seryl, threonyl, or tyrosyl residues, catalyzed by protein kinases, is thermodynamically spontaneous. Equally spontaneous is the hydrolytic removal of these phosphoryl groups by enzymes called protein phosphatases. 

Mammalian proteins are the targets of a wide range of covalent modification processes. Modifications such as glycosylation, hydroxylation, and fatty acid acylation introduce new structural features into newly synthesized proteins that tend to persist for the lifetime of the protein. Among the covalent modifications that regulate protein function (eg, methylation, adenylylation), the most common by far is phosphorylation-dephos-phorylation. Protein kinases phosphorylate proteins by... 

Figure 9-7. Covalent modification of a regulated enzyme by phosphorylation-dephosphorylation of a seryl residue.

The principal enzymes controlling glycogen metabolism—glycogen phosphorylase and glycogen synthase— are regulated by allosteric mechanisms and covalent modifications due to reversible phosphorylation and... 

The covalent modification of cellular proteins by phosphorylation of serine/ threonine and tyrosine residues provides an efficient molecular switch for altering cellular responses. 

We are very familiar with the idea of a large enzyme using a small molecule as its substrate. Here now we see an example of an enzyme that uses a protein as its substrate. Covalent modification, most frequently by phosphorylation, occurs when a controlling enzyme is itself a substrate for another enzyme, the modifying enzyme . 

This sort of control is usually achieved by either covalent modification (phosphorylation or de phosphorylation as in glycogen metabolism) or by proteolytic cleavage (e.g. activation of digestive enzymes in the gut, or blood clotting mechanism. 

Covalent modification of enzymes (molecular weight of several hundreds or thousands) by the incorporation of inorganic phosphate in the form of P03 (formula weight = 85), seems to represent a small chemical change in the enzyme yet is an important control mechanism of enzyme activity. Explain how phosphorylation can exert its controlling effect on the activity of the enzyme. 

Triglyceride and fatty acid synthesis are promoted by insulin stimulation of liver and adipose tissues by causing the phosphorylation of the first and controlling enzyme in the pathway acetyl-CoA carboxylase (see Section 6.3.2). This enzyme catalyses the formation of malonyl-CoA and requires both allosteric activation by citrate and covalent modification for full activity. 

Control of pymvate dehydrogenase activity is via covalent modification a specific kinase causes inactivation of the PDH by phosphorylation of three serine residues located in the pyruvate decarboxylase/dehydrogenase component whilst a phosphatase activates PDH by removing the phosphates. The kinase and phosphatase enzymes are non-covalently associated with the transacetylase unit of the complex. Here again we have an example of simultaneous but opposite control of enzyme activity, that is, reciprocal regulation. 

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