9OZD
Crystal structure of the polysaccharide lyase RbmB from Vibrio cholerae bound to Vibrio Polysaccharide
This is a non-PDB format compatible entry.
Summary for 9OZD
| Entry DOI | 10.2210/pdb9ozd/pdb |
| Descriptor | Polysaccharide lyase, {[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose, {[(2R,3S,4S)-3-acetamido-2,4-dihydroxy-3,4-dihydro-2H-pyran-6-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-{[(2R,3S,4R,5S,6R)-5-acetamido-3,4,6-trihydroxyoxane-2-carbonyl]amino}acetic acid (non-preferred name)-(1-4)-beta-D-glucopyranose, ... (8 entities in total) |
| Functional Keywords | polysaccharide lyase, beta-helix, periplasm, glycosidase, lyase |
| Biological source | Vibrio cholerae |
| Total number of polymer chains | 4 |
| Total formula weight | 177627.79 |
| Authors | Weerasekera, R.,Moreau, A.,Huang, X.,Potapova, A.,Schwechheimer, C.,Huynh, Y.,Cannizzo, O.,Gordon, R.,Hinbest, A.J.,Yang, Y.,Jiang, X.,Yan, J.,Yildiz, F.,Olson, R. (deposition date: 2025-06-05, release date: 2026-03-11, Last modification date: 2026-03-25) |
| Primary citation | Weerasekera, R.,Moreau, A.,Huang, X.,Potapova, A.,Schwechheimer, C.,Kandel, R.,Huynh, Y.,Cannizzo, O.,Gordon, R.,Gerace, E.,Hinbest, A.J.,Yang, Y.,Jiang, X.,Woods, R.J.,Yan, J.,Yildiz, F.H.,Olson, R. Crystal structure of Vibrio cholerae polysaccharide lyase RbmB bound to Vibrio polysaccharide (VPS) fragments provides insights into substrate recognition and cleavage. Proc.Natl.Acad.Sci.USA, 123:e2534280123-e2534280123, 2026 Cited by PubMed Abstract: Exopolysaccharides are carbohydrate polymers secreted by bacteria to perform various roles including adhesion to surfaces, protection from environmental stressors, and as key components in the production of biofilms. The human pathogen produces an exopolysaccharide called VPS, which is essential for the formation of its biofilm matrix through crosslinking interactions with a series of secreted accessory proteins. VPS consists of a repeating tetrasaccharide unit consisting of a uniquely modified α-L-gulose moiety (with N-acetyl, O-acetyl, and amide-linked glycine modifications). Encoded within the cluster containing the biofilm-production genes is a glycoside lyase called RbmB, which cleaves VPS and has been implicated in biofilm dispersal. Here we describe the ~2 Å X-ray structure of RbmB bound to tetrameric and octameric fragments of VPS representing 10 total monosaccharides of an enzyme-product complex. The structure, along with molecular dynamics simulations and complementary functional analyses of mutant proteins in vitro and in vivo, illustrates how recognition and cleavage of VPS relies on salt-bridging interactions between arginine residues in RbmB and the amide-linked glycine moiety uniquely found on the VPS L-gulose and a ~30° bend near the cleavage site that strains the scissile bond. We further present results regarding the localization of RbmB in cells, suggesting that cleavage of VPS by RbmB likely takes place in the periplasm. Sequence conservation suggests that homologous biofilm systems found in many species likely utilize a similar VPS cleavage mechanism suggesting that RbmB could be an effective tool for dispersing biofilms across the genus and beyond. PubMed: 41805565DOI: 10.1073/pnas.2534280123 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.62 Å) |
Structure validation
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