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Endo-β-1,3-glucanase plays an essential role in the deconstruction of β-1,3-<span style="font-variant: small-caps;">d</span>-glucan polysaccharides through hydrolysis. The gene (1650-bp) encoding a novel, bi-modular glycoside hydrolase family 64 (GH64) endo-β-1,3-glucanase (GluY) with a ricin-type β-trefoil lectin domain (RICIN)-like domain from <i>Cellulosimicrobium funkei</i> HY-13 was identified and biocatalytically characterized. The recombinant enzyme (rGluY: 57.5 kDa) displayed the highest degradation activity for laminarin at pH 4.5 and 40 °C, while the polysaccharide was maximally decomposed by its C-terminal truncated mutant enzyme (rGluYΔRICIN: 42.0 kDa) at pH 5.5 and 45 °C. The specific activity (26.0 U/mg) of rGluY for laminarin was 2.6-fold higher than that (9.8 U/mg) of rGluYΔRICIN for the same polysaccharide. Moreover, deleting the C-terminal RICIN domain in the intact enzyme caused a significant decrease (>60%) of its ability to degrade β-1,3-<span style="font-variant: small-caps;">d</span>-glucans such as pachyman and curdlan. Biocatalytic degradation of β-1,3-<span style="font-variant: small-caps;">d</span>-glucans by inverting rGluY yielded predominantly <span style="font-variant: small-caps;">d</span>-laminaripentaose. rGluY exhibited stronger growth inhibition against <i>Candida albicans</i> in a dose-dependent manner than rGluYΔRICIN. The degree of growth inhibition of <i>C. albicans</i> by rGluY (approximately 1.8 μM) was approximately 80% of the fungal growth. The superior anti-fungal activity of rGluY suggests that it can potentially be exploited as a supplementary agent in the food and pharmaceutical industries.