Structure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in plant cell wall breakdown

Abstract 

Saccharophagus degradans belongs to a recently discovered group of marine bacteria equipped with an arsenal of sugar cleaving enzymes coupled to carbohydrate-binding domains to degrade various insoluble complex polysaccharides. The modular Sde-1182 protein consists of a family 2 carbohydrate binding module linked to a X158 domain of unknown function. The 1.9Å and 1.55Å resolution crystal structures of the isolated X158 domain bound to the two related polyisoprenoid molecules, ubiquinone and octaprenyl pyrophosphate, unveil a β-barrel architecture reminiscent of the YceI-like superfamily that resembles the architecture of the lipocalin fold. This unprecedented association coupling oxidoreduction and carbohydrate recognition events may have implications for effective nutrient uptake in the marine environment.

Abbreviations: 8PP, 2-octaprenyl 6-hydroxyphenol, OPP, all-trans C40-octaprenyl pyrophosphate, UQ-8, ubiquinone-8, CBM, carbohydrate binding module, PEG, polyethylene glycol, SAD, single-wavelength anomalous dispersion, IPTG, isopropyl β-D-1-thiogalactopyranoside, rmsd, root mean square deviation

Keywords: Crystal structure, Polyisoprenoid transport, Plant cell wall degradation, Carbohydrate binding module, Ubiquinone-8, Oxydoreduction, Saccharophagus degradans