Endo-fucoidanases are important in structural analysis of fucoidans and preparation of fuco-oligosaccharides. However their enzymological properties and analysis of degradation products are scarcely investigated. Truncated endo-alpha (1 -> 3)-fucoidanase Fda1 (tFda1B from Alteromonas sp. was overexpressed and characterized, showing highest activity at pH 7.0, 35 degrees C, and 1.0 M NaCl. Its K-m and k(cat) were 3.88 +/- 0.81 mg/mL and 0.82 +/- 0.17 min(-1). Fe3+ and Mn2+ enhanced activity by 100% and 19.5% respectively. Co2+ and Cu2+ completely inactivated tFda1B, whereas Ni2+, Mg2+, Zn2+, Pb2+, Ca2+, Ba2+ and Li+ decreased activity by 58.8%, 56.0%, 50.6%, 47.7%, 28.9%, 15.6% and 37.5%, respectively. Catalytic residues were identified through structure and sequence alignment, and confirmed by mutagenesis. Degradation products of Kjellmaniella crassifolia fucoidan by tFda1B were characterized by LC-ESI-MS/MS, confirming tFda1B belongs to endo-(1 -> 3)-fucoidanases, and backbone of K. crassifolia fucoidan is 1 -> 3 fucoside linkage. This endo-alpha (1 -> 3)-fucoidanase would be useful for elucidating fucoidan structures, and be used as a food enzyme.