A COMPARATIVE-ANALYSIS OF THE PRIMARY SEQUENCES AND CHARACTERISTICS OF HEPARINASE-I, HEPARINASE-II, AND HEPARINASE-III FROM FLAVOBACTERIUM-HEPARINUM

Heparinases I, II and III from F. heparinum cleave heparin-like molecu les, with a high degree of substrate specificity, at the glucosamine-u ronate linkage by elimination, leaving an unsaturated C4-C5 bond in th e uronic acid. The primary sequence of these enzymes have been reporte d earlier. In this study we perform a comparative analysis of the prop erties and primary sequences of heparinase I, II and III. Alignment of the primary sequences revealed little sequence homology (15% residue identity in a LALIGN alignment) at both DNA and amino acid levels. The re are three basic clusters in heparinase II satisfying the heparin bi nding consensus sequence with one of the sequences sharing homology wi th a consensus sequence in the heparin binding site of heparinase I an d two basic clusters in heparinase III. Similar to heparinase I, there are two putative 'EF-hand' calcium coordinating motifs in heparinase II, while heparinase II does not contain any such motifs. Recombinant heparinases II and III's degradation of the substrate and the subseque nt separation of the oligosaccharide products by POROS anion exchange chromatography were identical to those obtained from native heparinase s II and III from F. heparinum. (C) 1996 Academic Press