Domain

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A protein domain usually means a sequence of amino acids that folds, independently of the remainder of the full-length sequence, into a compact stable structure. Water-soluble domains typically have hydrophobic cores. Some small full-length proteins consist of a single domain, but many proteins have two or more domains. A domain is typically 100-250 amino acids in length[1], but can sometimes be shorter or longer.

In 2006, chains with a single domain in the CATH database had an average length of 159[2]. In 2006, 64% of all protein structures in CATH were single domain chains. 27% were two-domain chains[2].

Examples:

  • 9ins (porcine): Insulin, with 51 amino acids, is one of the smallest stably folded protein domains, on the boundary between a protein and a peptide. It has a hydrophobic core. Human preproinsulin is synthesized with 110 amino acids. After removal of a 24 amino acid signal sequence, the remaining 86 amino acid proinsulin is cleaved in two places, forming a mature disulfide-linked dimer of two protein chains. Chain B is residues 1-30. Chain A is residues 66-86 (length 21). "C-peptide", residues 33-63 (length 31), is released as a separate bio-active peptide. Mature human insulin differs from porcine in a single amino acid: the terminal residue in chain B is Thr vs. Ala, respectively. Wikipedia has good articles on insulin synthesis and C-peptide. See also Insulin Structure & Function.
  • 1lzs: Lysozyme functions as a single chain of 130 amino acids. It folds to single domain with a hydrophobic core.
  • 2hhd: Each of the 4 chains that form hemoglobin (a tetramer) folds into a single domain composed of alpha-helices. Each domain (chain) is 141-146 amino acids in length for human hemoglobin.
  • 1igy: Immunoglobulin G (antibody) consists of 12 domains in 4 chains. These immunoglobulin superfamily domains are composed of beta-sheets. Each of the two heavy chains has 4 domains, and each of the 2 light chains has 2 domains. These domains are about 110 amino acids in length. Each heavy chain has two pairs of domains connected by a flexible linker about 20 amino acids in length.

For more information see Protein Domain in Wikipedia.

See also [1] and this summary of it.

References

  1. ↑ 1.0 1.1 Evolution of the protein repertoire. Cyrus Chothia, Julian Gough, Christine Vogel, Sarah A. Teichmann (2003). Science 300:1701-3. PMID:12805536
  2. ↑ 2.0 2.1 Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res. 2007 Jan;35(Database issue):D291-7. doi: 10.1093/nar/gkl959., Epub 2006 Nov 29. PMID:17135200 doi:http://dx.doi.org/10.1093/nar/gkl959

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