Cells often regulate proteins by covalently adding and removing phosphate groups.

A protein kinase transfers a phosphoryl group, usually from ATP, onto a target protein. In eukaryotic signaling, common target residues are serine, threonine and tyrosine side chains containing hydroxyl groups.

A simplified reaction is

$$\mathrm{protein{-}OH+ATP\rightarrow protein{-}OPO_3^{2-}+ADP}.$$

A protein phosphatase catalyzes removal of the phosphate by hydrolysis.

Phosphorylation changes interactions, not merely mass

A phosphate group introduces substantial negative charge and new hydrogen-bonding possibilities. Depending on the protein and site, phosphorylation can

• activate or inhibit catalytic activity;
• create or destroy a binding site;
• change protein localization;
• alter protein conformation or stability.

There is no universal rule that phosphorylation means activation.

Kinases and phosphatases form a reversible switch

unphosphorylated protein
       ↓ kinase + ATP
phosphorylated protein
       ↓ phosphatase
unphosphorylated protein

Because different enzymes control the forward and reverse transformations, cells can regulate each direction independently.

Example

Suppose an enzyme is active only when phosphorylated. Activating its kinase increases the fraction of active enzyme, while activating the corresponding phosphatase decreases it. No new copy of the enzyme must be synthesized, so the response can be rapid.

If the phosphorylated form were instead inactive, the same chemical cycle would implement the opposite regulatory logic.

Cascades are possible

A kinase can itself be regulated by phosphorylation. One activated kinase can then phosphorylate many molecules of a downstream kinase, creating a phosphorylation cascade.

Protein phosphorylation is therefore a reusable covalent regulatory mechanism. The biological meaning comes from which protein and site are modified and what that modification does to molecular interactions.