4KMI

Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with PO4

Summary for 4KMI

• Entry DOI: 10.2210/pdb4kmi/pdb
• Related: 3WAS 3WAT 3WAU
• Descriptor: 4-O-beta-D-mannosyl-D-glucose phosphorylase, PHOSPHATE ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
• Functional Keywords: 5-bladed beta propeller fold, phosphorylase, mannan biodegradation, transferase
• Biological source: Bacteroides fragilis
• Total number of polymer chains: 2
• Total formula weight: 88685.45

Authors

Nakae, S.,Ito, S.,Higa, M.,Senoura, T.,Wasaki, J.,Hijikata, A.,Shionyu, M.,Ito, S.,Shirai, T. (deposition date: 2013-05-08, release date: 2013-09-04, Last modification date: 2023-11-08)

Primary citation

Nakae, S.,Ito, S.,Higa, M.,Senoura, T.,Wasaki, J.,Hijikata, A.,Shionyu, M.,Ito, S.,Shirai, T.
Structure of Novel Enzyme in Mannan Biodegradation Process 4-O-beta-d-Mannosyl-d-Glucose Phosphorylase MGP
J.Mol.Biol., 425:4468-4478, 2013

PubMed Abstract: The crystal structure of a novel component of the mannan biodegradation system, 4-O-β-D-mannosyl-D-glucose phosphorylase (MGP), was determined to a 1.68-Å resolution. The structure of the enzyme revealed a unique homohexameric structure, which was formed by using two helices attached to the N-terminus and C-terminus as a tab for sticking between subunits. The structures of MGP complexes with genuine substrates, 4-O-β-D-mannosyl-D-glucose and phosphate, and the product D-mannose-1-phosphate were also determined. The complex structures revealed that the invariant residue Asp131, which is supposed to be the general acid/base, did not exist close to the glycosidic Glc-O4 atom, which should be protonated in the catalytic reaction. Also, no solvent molecule that might mediate a proton transfer from Asp131 was observed in the substrate complex structure, suggesting that the catalytic mechanism of MGP is different from those of known disaccharide phosphorylases.

PubMed: 23954514
DOI: 10.1016/j.jmb.2013.08.002

Experimental method

X-RAY DIFFRACTION (1.8 Å)