7KS6
STRUCTURE OF TETRASACCHARIDE BUILDING BLOCK OF A SULFATED FUCAN FROM LYTECHINUS VARIEGATUS
Summary for 7KS6
| Entry DOI | 10.2210/pdb7ks6/pdb |
| Descriptor | 4-O-sulfo-alpha-L-fucopyranose-(1-3)-2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose (1 entity in total) |
| Functional Keywords | sulfated fucan, tetrasaccharide, carbohydrate, carbohydrate unit |
| Biological source | Lytechinus variegatus |
| Total formula weight | 1002.90 |
| Authors | Kim, S.B.,Thara, R.,Aderibigbe, A.O.,Doerksen, R.J.,Pomin, V.H. (deposition date: 2020-11-21, release date: 2020-12-16, Last modification date: 2024-05-01) |
| Primary citation | Bezerra, F.F.,Vignovich, W.P.,Aderibigbe, A.O.,Liu, H.,Sharp, J.S.,Doerksen, R.J.,Pomin, V.H. Conformational properties of l-fucose and the tetrasaccharide building block of the sulfated l-fucan from Lytechinus variegatus. J.Struct.Biol., 209:107407-107407, 2020 Cited by PubMed Abstract: Although the 3D structure of carbohydrates is known to contribute to their biological roles, conformational studies of sugars are challenging because their chains are flexible in solution and consequently the number of 3D structural restraints is limited. Here, we investigate the conformational properties of the tetrasaccharide building block of the Lytechinus variegatus sulfated fucan composed of the following structure [l-Fucp4(SO)-α(1-3)-l-Fucp2,4(SO)-α(1-3)-l-Fucp2(SO)-α(1-3)-l-Fucp2(SO)] and the composing monosaccharide unit Fucp, primarily by nuclear magnetic resonance (NMR) experiments performed at very low temperatures and using HO as the solvent for the sugars rather than using the conventional deuterium oxide. By slowing down the fast chemical exchange rates and forcing the protonation of labile sites, we increased the number of through-space H-H distances that could be measured by NMR spectroscopy. Following this strategy, additional conformational details of the tetrasaccharide and l-Fucp in solution were obtained. Computational molecular dynamics was performed to complement and validate the NMR-based measurements. A model of the NMR-restrained 3D structure is offered for the tetrasaccharide. PubMed: 31698075DOI: 10.1016/j.jsb.2019.107407 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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