Fig. 3: BxMAG GH16_17 form functionally distinct clades to saccharify carrageenan subtypes. | Nature Communications

Fig. 3: BxMAG GH16_17 form functionally distinct clades to saccharify carrageenan subtypes.

From: Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome

Fig. 3: BxMAG GH16_17 form functionally distinct clades to saccharify carrageenan subtypes.The alternative text for this image may have been generated using AI.

A SACCHARIS v2 generated phylogeny of GH16_17 members from BxMAGBOV, and BxCar5BOV and BxCar17BOV within this study aligned to characterized GH16_17 members from the CAZy database (www.cazy.org). Signal peptides of BxCar enzymes are denoted by † (SPI) and ‡.(SPII) B Structural analysis of BxMAGBov GH16_17A. Left: Overlay of the structure of BxMAGBOV GH16_17A (orange) with the GH16_17 κ-carrageenase from Pseudoalteromonas carrageenovora (blue; PDB ID 5OCQ). Key residues within only the -1 and -2 subsites are shown as sticks with the residues acting as nucleophile or acid/base labeled and indicated with superscript “n” or “a”, respectively. The substitution in BxMAGBOV GH16_17A blocking accommodation of the 4S group is shown as a magenta stick. Right: Overlay of the structure of BxMAGBOV GH16_17A (orange) with the GH16_13 β/κ-carrageenase from Wenyingzhuangia fucanilytica (gray; PDB ID 9INT). C Surface representations of the -1 subsites of 5OCQ (top), BxMAGBOV GH16_17A (middle), and an AlphaFold 334 generated model of BxMAGBOV GH16_17B, respectively. The ligand in 5OCQ is shown; ligands in BxMAGBOV GH16_17A and the BxMAGBOV GH16_17B model are derived from overlays with 5OCQ. D The activity of PfGH16B (an α/β-carrageenan specific GH16_13)35 and BxMAGBOV GH16_17A on ι-carrageenan (Left) and on ι-carrageenan pretreated with PfS1_19B to remove 4S modifications (Right) as examined by fluorophore-assisted carbohydrate electrophoresis (n = 3). Gels were processed in parallel. E BxMAGBOV GH16_17B digests of MjEx were analyzed by LC-ESI-MS, and example extracted ion chromatograms are shown. F ESI-MS/MS with HCD was performed in order to identify the extracted ions. The MS2 product ion spectra shown are consistent with neo-κ/ι-hybrid tetrasaccharide, the majority enzymatic product from the MjEx. Monosaccharide symbols are displayed according to the Symbol Nomenclature for Glycans system101. Source data are provided as a Source Data file.

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