APPENDIX ONE - Glossary of Protein Domains

Summary

All protein domains that were mentioned in the text or tables are inventoried below. For further information, consult PROSITE (www.expasy.ch/prosite) or the following reviews: domains in general, DNA-binding domains, scaffolding domains, extracellular domains, domain classification, domain evolution, protein-protein binding, protein-peptide binding, receptor-ligand binding, signal transduction, and an inventory of fly protein domains.

D. melanogaster proteins vary in size from 21 a.a. (L38, a ribosomal protein) to 5201 a.a. (Kakapo, a cytoskeletal component needed for intercellular adhesion). The domains listed below vary from 4 a.a. (WRPW) to ∼270 a.a. (PAS).

N.B.: Customarily, “domain” denotes a motif in proteins, while “box” refers to DNA. Thus, for example, the homeobox encodes the homeodomain. “Repeat” does not connote identity within a protein (e.g., only 6 of the 38 residues are invariant among Notch's 36 EGF-like repeats), nor does it imply interchangeability. For instance, the LIM domains of Lim3 can replace those of Apterous in wing development but not in the CNS. Likewise, Cactus's ankyrin repeats cannot functionally substitute for those of Notch. The specificity of repeats is epitomized by the “arm” domain:

Although individual repeats within a single protein are only about 30% identical, they are highly conserved during evolution. Thus, corresponding repeats of armadillo and β-catenin (which are direct homologs) are very similar (e.g., repeat 1 of armadillo is 90% identical to repeat 1 of β-catenin). […]