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• A truncated endo -α(1 → 3)-fucoidanase was expressed and characterized in detail. • Catalytic residues of endo -α(1 → 3)-fucoidanase were identified and confirmed. • Degraded products of fucoidan by α(1 → 3)-fucoidanase were characterized by ESI-MS2. • Kjellmaniella crassifolia fucoidan is complex and composed of α(1 → 3) linked l -fucose. 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 - α (1 → 3)-fucoidanase Fda1 (tFda1B from Alteromonas sp. was overexpressed and characterized, showing highest activity at pH 7.0, 35 °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 - α (1 → 3)-fucoidanase would be useful for elucidating fucoidan structures, and be used as a food enzyme. [ABSTRACT FROM AUTHOR]