A protein domain is a conserved part of a specific protein sequence and structure that can function exist and evolve independently of the rest of the protein chain. Each protein domain forms a compact three-dimensional structure and can be independently stable and folded. A protein often consists of several structural domains. A protein domain may appear in several different proteins. Domains were used as building blocks in molecular evolution and these may be recombined in different ways to create proteins with different functions. Domains vary in length from between about 25 amino acids up to 500 amino acids. The shortest domains such as zinc fingers are stabilized by metal ions or disulfide bridges. Domains often shape functional units, such as the calcium-binding EF hand domain of calmodulin. Since domains are independently stable, they can be "exchanged" by genetic engineering between two proteins to create imaginary proteins.
For instance, Eukaryotic Argonaute proteins consist of four domains: the N-terminal, PAZ, MID and PIWI domains (see Fig. a). In some cases, especially for the structures of Piwi protein form Archaeoglobus fulgidus (AfPiwi), the MID domain and PIWI domain have been called domain A and domain B, respectively. A crystal structure of Pyrococcus furiosus Argonaute (Ago) soaked with Mn2+(PDB identity 1Z25) is shown in Fig. b. The protein adopts a bilobate architecture, with PAZ and the N-terminal domains forming one lobe and the PIWI and MID domains forming the other. The metal ion in the active site is shown as a purple sphere format. The amino-acid residues related to metal-ion binding in the slicer catalytic site are shown in colored stick.
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