The three major isoforms of human apolipoprotein E (apo-E2, -E3, and -E4) are coded for by three alleles (E2, E3, and E4) which have a common genetic locus. Previously, we demonstrated that E2, E3, and E4 differ in primary structure from one another at two substitution sites, site A (residue 112) and site B (residue 158). At sites A/B, apo-E2, -E3, and -E4 contain cysteine/cysteine, cysteine/arginine, and arginine/arginine, respectively. We demonstrated that the substitution of cysteine for arginine at site B is at least partly responsible for the defective binding of apo-E2 to human fibroblast low density lipoprotein receptors, compared to the normal binding activity ofapo-E3 or -E4. Subjects with the genetic disorder type m hyperlipoproteinemia are phenotypically homozygous for apo-E2, but the binding activity of apo-E to the fibroblast receptor differs considerably from one type HI individual to another. We therefore undertook a partial comparative sequence analysis of apo-E2 from three type ]II subjects whose apo-E displayed this heterogeneity. The subject with the poorest binding apo-E2 was genotypically homozygous for an apo-E allele (ÂŁ2); cysteine was found at sites A and B. The subject with the most active apo-E2 was genotypically homozygous for an apo-E allele (E2*); cysteine was found at site A and at a new site (site C, residue 145). The ÂŁ2* allele specifies a protein that has arginine at site B (residue 158); the e2 allele specifies a protein that has arginine at site C (residue 145). Therefore, the two alleles differ from one another by cysteine/arginine interchanges at two positions, sites B and C. The third subject, whose apo-E2 displayed binding activity intermediate between the activities of the other two, was genotypically heterozygous, having one E2 allele and one E2* allele. The intermediate binding activity of apo-E2 from this subject resulted from having a mixture of severely defective apo-E (specified by E2) and slightly defective apo-E (specified by E2*). (13,14), demonstrating that the alleles controlling the expression of these isoforms are the structural genes for apo-E. The E2, E3, and E4 isoforms differ by virtue ofamino acid substitutions at two sites in the protein, involving cysteine/arginine interchanges. The E3 isoform has a cysteine at site A (residue 112) and an arginine at site B (residue 158). However, the E2 isoform from a type III subject has cysteine at both sites (14). The E4 isoform lacks cysteine entirely and contains arginine at both residues 112 and 158, as determined by partial sequence analysis (unpublished data). Therefore, the E2 and E4 isoforms each differ from E3 by a single amino acid substitution (13,14). It has been shown that apo-E2 from subjects with type III hyperlipoproteinemia does not bind to the apo-B,E [low density lipoprotein (LDL)] receptors of human fibroblasts as well as E3 and E4, which are equally active (15, 16). Furthermore, it has been shown that the substitution at site B (cysteine for arginine) in the sequence ofthe E2 isoform is...