6sgf | pdb_00006sgf

Molecular insight into a new low affinity xylan binding module CBM86, from the xylanolytic gut symbiont Roseburia intestinalis.

spinqualitylabelsall models 6sgf, resolution 1.76Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6sgf is a 6 chain structure with sequence from Roseburia intestinalis l1-82. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CD, CL, XYP Gene: ROSINTL182_06494 (Roseburia intestinalis L1-82) Activity: Endo-1,4-beta-xylanase, with EC number 3.2.1.8 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Efficient capture of glycans, the prime metabolic resources in the human gut, confers a key competitive advantage for gut microbiota members equipped with extracellular glycoside hydrolases (GHs) to target these substrates. The association of glycans to the bacterial cell surface is typically mediated by carbohydrate binding modules (CBMs). Here we report the structure of RiCBM86 appended to a GH10 xylanase from Roseburia intestinalis. This CBM represents a new family of xylan binding CBMs present in xylanases from abundant and prevalent healthy human gut Clostridiales. RiCBM86 adopts a canonical beta-sandwich fold, but shows structural divergence from known CBMs. The structure of RiCBM86 has been determined with a bound xylohexaose, which revealed an open and shallow binding site. RiCBM86 recognizes only a single xylosyl ring with direct hydrogen bonds. This mode of recognition is unprecedented amongst previously reported xylan-binding type-B CBMs that display more extensive hydrogen-bonding patterns to their ligands or employ Ca(2+) to mediate ligand binding. The architecture of RiCBM86 is consistent with an atypically low binding affinity (KD approximately 0.5 mM for xylohexaose) compared to most xylan binding CBMs. Analyses using NMR spectroscopy corroborated the observations from the complex structure and the preference of RiCBM86 to arabinoxylan over glucuronoxylan, consistent with the largely negatively charged surface flanking the binding site. Mutational analysis and affinity electrophoresis established the importance of key binding residues, which are conserved in the family. This study provides novel insight into the structural features that shape low-affinity CBMs that mediate extended bacterial glycan capture in the human gut niche. Molecular insight into a new low affinity xylan binding module from the xylanolytic gut symbiont Roseburia intestinalis.,Leth ML, Ejby M, Madland E, Kitaoku Y, Slotboom DJ, Guskov A, Aachmann FL, Abou Hachem M FEBS J. 2019 Nov 6. doi: 10.1111/febs.15117. PMID:31693302 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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