Table 3.
Structure | Dynamozones | Proteins | Role or Function | References |
---|---|---|---|---|
Loop | Flap |
• HIV protease • Plasmepsins • Beta-secretase • Cathepsin • Pepsins |
These regions control the entrance and stabilization of ligands in the active site | 67–70 |
Loop | Loop (Residues 166–176) | • Triosephosphate isomerase | In the ligand-bound state, the loop moves for ∼7 Å as a rigid lid toward the active site and accepts a “closed” conformation. These motions of the rigid lid close to the active site are essential for the catalytic mechanism of the enzyme | 71–73 |
Loop | Loop |
• Enolases • Aldolases |
Movements of the loop permit the catalytic residues to be oriented in a suitable position for catalysis | 74–76 |
Loop | WPD loop | • Protein tyrosine phosphatases (PTPs) | This loop closes over the active site upon binding of the substrate, and loop closure permits the correct orientation of catalytic residues around the ligand | 77,78 |
Loop | Met20 loop (Active site loop ( | • Dihydrofolate reductase (DHFR) | This loop acts as a lid that closes on the cofactor, thereby allowing DHFR to adopt occluded and closed conformations | 79–81 |
Loop | Helical loop | • Lipases | This loop is important for the enzyme function, acting as a lid to open or close the hydrophobic active site | 82,83 |
Loop | Long loop | • β1,4-galactosyl transferase | A displacement of more than 20 Å this long loop in protein provides binding sites for various ligands | 84 |
Loop | Omega loop | • Cdc34-like E2 enzymes | This loop can act as a lid that regulates the accessibility of the catalytic site and disturbs the charging activity of ubiquitin until a conformational change toward an open state is promoted by phosphorylation | 85–87 |
Linker | Flexible linker | • Calmodulin (CaM) | CaM has two globular domains connected by a short and flexible linker that permits the protein to accept a wide variety of extended and compact conformations | 88–90 |
Hinge Loop Linker |
• Hinge region • P-loop • hydrophobic “spines” • A-loop • αC helix • DFG motif • αB helix |
• Protein kinases (PKs) • Tyrosin kinase • Src protein kinase |
Hinge region: The hinge motion is necessary for the opening and closure of the kinase catalytic domain (CD) P-loop (β1-β2 loop or G-loop or Gly-rich loop): This flexible loop is very important for the coordination of ATP phosphates Hydrophobic “spines”: Two hydrophobic “spines” link the two lobes of protein kinase and dynamically connect all the elements important for catalysis A-loop (Activation loop): In the inactive state of the enzyme, the A-loop is folded onto itself, and its opening is required to create the catalytically active form αC helix: This helix in the “in” active conformation forms a hydrogen bond with the β3 strand for creating the catalytically active form of the enzyme DFG motif: This motif in the active site switches from an inactive (DFG-out) conformation to an active (DFG-in) conformation, which is necessary to create the catalytically active form of the enzyme αB helix: This helix creates a cavity, the so-called PIF pocket, which is very important for allosteric regulation of the protein kinases belonging to the AGC family |
91–96 |
Hinge | Hinge region | • Lactoferrin | The hinge motions permit the formation of the complete iron-binding site in the closed states of lactoferrin | 97–100 |
Hinge | Hinge region | • Immunoglobulins | The hinge region is connecting the Fab (Fragment antigen binding) region to the Fc (Fragment crystallizable) region | 101,102 |