title: Evolution of distinct EGF domains with specific functions.
abstract: EGF domains are extracellular protein modules cross-linked by three intradomain disulfides. Past studies suggest the existence of two types of EGF domain with three-disulfides, human EGF-like (hEGF) domains and complement C1r-like (cEGF) domains, but to date no functional information has been related to the two different types, and they are not differentiated in sequence or structure databases. We have developed new sequence patterns based on the different C-termini to search specifically for the two types of EGF domains in sequence databases. The exhibited sensitivity and specificity of the new pattern-based method represents a significant advancement over the currently available sequence detection techniques. We re-annotated EGF sequences in the latest release of Swiss-Prot looking for functional relationships that might correlate with EGF type. We show that important post-translational modifications of three-disulfide EGFs, including unusual forms of glycosylation and post-translational proteolytic processing, are dependent on EGF subtype. For example, EGF domains that are shed from the cell surface and mediate intercellular signaling are all hEGFs, as are all human EGF receptor family ligands. Additional experimental data suggest that functional specialization has accompanied subtype divergence. Based on our structural analysis of EGF domains with three-disulfide bonds and comparison to laminin and integrin-like EGF domains with an additional inter-domain disulfide, we propose that these hEGF and cEGF domains may have arisen from a four-disulfide ancestor by selective loss of different cysteine residues.
authors.affiliation: Computational Biology and Bioinformatics Program, Victor Chang Cardiac Research Institute, 384 Victoria St., Darlinghurst, Sydney, NSW 2010, Australia. m.wouters@victorchang.unsw.edu.au
authors.forename: Merridee A
authors.initials: MA
authors.lastname: Wouters
authors.forename: Isidore
authors.initials: I
authors.lastname: Rigoutsos
authors.forename: Carmen K
authors.initials: CK
authors.lastname: Chu
authors.forename: Lina L
authors.initials: LL
authors.lastname: Feng
authors.forename: Duncan B
authors.initials: DB
authors.lastname: Sparrow
authors.forename: Sally L
authors.initials: SL
authors.lastname: Dunwoodie
mesh_terms: D000595:Amino Acid Sequence; D015923:Complement C1r / Q000737:chemistry; D030562:Databases, Protein; D004815:Epidermal Growth Factor / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D019143:Evolution, Molecular; D006031:Glycosylation; D006801:Humans; D006900:Hydroxylation; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry; D053779:Latent TGF-beta Binding Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D047908:Intracellular Signaling Peptides and Proteins; D053779:Latent TGF-beta Binding Proteins; D004815:Epidermal Growth Factor; D015923:Complement C1r