Substrate binding sites or catalytic sites of multi-domain proteins are often situated within a cleft between two domains. Relative, rigid body movements between the two adjacent domains allows an induced-fit binding of the substrate and the creation of a catalytic environment that is isolated from the solvent.
A few examples:
1. the bi-lobal monomeric aspartic proteinase, pepsin, and the dimmeric HIV proteinase which possesses similar activities.
2. porphobilinogen deaminase
3. calmodulin, free and bound to a helical peptide
Gerstein, Lesk and Chothia describe many more examples of domain movements involved in induced fit binding.
M. Gerstein, A.M. Lesk and C. Chothia (1994). Structural mechanisms for domain movement in proteins. Biochemistry, 33, 6739-6749.
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