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MASP-3 (mannose/mannan binding lectin (MBL) associated serine protease-3) is ~82 kDa protein generated through alternative splicing of the MASP1 gene. This gene also generates MASP-1 and MAp44 proteins. MASP-3 is bound to multimeric forms of pathogen receptors, such as MBL and the three ficolins. MASP-3 has two CUB, a calcium-binding EGF-like, a trypsin-like serine protease and two complement control protein (CCP) domains. The serine protease domain however, is not known to be active and does not act on substrates of either MASP-1 or MASP-2. Instead, it competes with MASP-1 and MASP-2 to bind to MBL and therefore plays a regulatory role in the lectin pathway of complement activation. In mice however, MASP-3 can activate the alternative complement pathway, by directly activating complement factor D (fD).

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