4UDI

Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.85 Angstrom from unknown human gut bacteria (Uhgb_MP)

Summary for 4UDI

• Entry DOI: 10.2210/pdb4udi/pdb
• Related: 4UDG 4UDJ 4UDK
• Descriptor: UHGB_MP, PHOSPHATE ION, GLYCEROL, ... (7 entities in total)
• Functional Keywords: transferase, glycoside hydrolase family 130, b-1, 4-mannopyranosyl-chitobiose phosphorylase, n-glycan phosphorolysis
• Biological source: UNCULTURED ORGANISM
• Total number of polymer chains: 6
• Total formula weight: 240973.43

Authors

Ladeveze, S.,Cioci, G.,Potocki-Veronese, G.,Tranier, S.,Mourey, L. (deposition date: 2014-12-10, release date: 2015-05-27, Last modification date: 2023-12-20)

Primary citation

Ladeveze, S.,Cioci, G.,Roblin, P.,Mourey, L.,Tranier, S.,Potocki-Veronese, G.
Structural Bases for N-Glycan Processing by Mannoside Phosphorylase.
Acta Crystallogr.,Sect.D, 71:1335-, 2015

PubMed Abstract: The first crystal structure of Uhgb_MP, a β-1,4-mannopyranosyl-chitobiose phosphorylase belonging to the GH130 family which is involved in N-glycan degradation by human gut bacteria, was solved at 1.85 Å resolution in the apo form and in complex with mannose and N-acetylglucosamine. SAXS and crystal structure analysis revealed a hexameric structure, a specific feature of GH130 enzymes among other glycoside phosphorylases. Mapping of the -1 and +1 subsites in the presence of phosphate confirmed the conserved Asp104 as the general acid/base catalytic residue, which is in agreement with a single-step reaction mechanism involving Man O3 assistance for proton transfer. Analysis of this structure, the first to be solved for a member of the GH130_2 subfamily, revealed Met67, Phe203 and the Gly121-Pro125 loop as the main determinants of the specificity of Uhgb_MP and its homologues towards the N-glycan core oligosaccharides and mannan, and the molecular bases of the key role played by GH130 enzymes in the catabolism of dietary fibre and host glycans.

PubMed: 26057673
DOI: 10.1107/S1399004715006604

Experimental method

X-RAY DIFFRACTION (1.8 Å)