title: The geometry of domain combination in proteins.
abstract: Most proteins in genomes are the result of the recombination of two or more domains. It has been found that if proteins are formed by a combination of domains from superfamilies A and B, then the domains may occur in the sequential order AB or BA but only in about 2% of cases do they occur in both sequential orders. The classical Rossmann domains of known structure are combined with catalytic domains from seven different superfamilies. In addition, there are eight cases where structures with both AB and BA domain combinations are known. For these two sets of structures, we analysed: (i) the relative orientation of the domains; (ii) the type of domain connection; (iii) the structure of the interdomain links; and (iv) domain function. The results of this analysis indicate that in most cases domain order is conserved because recombination of the domains has only occurred once during the course of evolution. Functional reasons become important when the domain connections are short. In seven out of the eight known cases where domains are combined in the AB and BA sequential orders they have different geometrical relationships that give them different functional properties.
authors.affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Bashton@mrc-lmb.cam.ac.uk
authors.forename: Matthew
authors.initials: M
authors.lastname: Bashton
authors.forename: Cyrus
authors.initials: C
authors.lastname: Chothia
mesh_terms: D000818:Animals; D020134:Catalytic Domain; D017124:Conserved Sequence; D030562:Databases, Protein; D019143:Evolution, Molecular; D008958:Models, Molecular; D005810:Multigene Family; D009243:NAD / Q000378:metabolism; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D011995:Recombination, Genetic; D012984:Software; D013329:Structure-Activity Relationship; D018909:src Homology Domains
chemical_list: D011506:Proteins; D009243:NAD