The Structural Bases of the Processive Degradation of ι-Carrageenan, a Main Cell Wall Polysaccharide of Red Algae

ι-Carrageenans are sulfated 1,3-α-1,4-β-galactans from the cell walls of red algae, which auto-associate into crystalline fibers made of aggregates of double-stranded helices. ι-Carrageenases, which constitute family 82 of glycoside hydrolases, fold into a right-handed β-helix. Here, the structure of Alteromonas fortis ι-carrageenase bound to ι-carrageenan fragments was solved at 2.0 Å resolution (PDB 1KTW). The enzyme holds a ι-carrageenan tetrasaccharide (subsites +1 to +4) and a disaccharide (subsites −3, −4), thus providing the first direct determination of a 3D structure of ι-carrageenan. Electrostatic interactions between basic protein residues and the sulfate substituents of the polysaccharide chain dominate ι-carrageenan recognition. Glu245 and Asp247 are the proton donor and the base catalyst, respectively. C-terminal domain A, which was highly flexible in the native enzyme structure, adopts a α/β-fold, also found in DNA/RNA-binding domains. In the substrate–enzyme complex, this polyanion-binding module shifts toward the β-helix groove, forming a tunnel. Thus, from an open conformation which allows for the initial endo-attack of ι-carrageenan chains, the enzyme switches to a closed-tunnel form, consistent with its highly processive character, as seen from the electron-microscopy analysis of the degradation of ι-carrageenan fibers.