title: Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.
abstract: In Ruminococcus albus, 4-O-β-D-mannosyl-D-glucose phosphorylase (RaMP1) and β-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze β-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-O-β-D-mannosyl-d-glucose and RaMP2 with/without β-(1→4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding.
authors.affiliation: Graduate School of Life Science, Hokkaido University, Sapporo, Japan.
authors.forename: Yuxin
authors.initials: Y
authors.lastname: Ye
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Saburi
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.
authors.forename: Rei
authors.initials: R
authors.lastname: Odaka
authors.affiliation: Graduate School of Life Science, Hokkaido University, Sapporo, Japan.|Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Kato
authors.affiliation: Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
authors.forename: Naofumi
authors.initials: N
authors.lastname: Sakurai
authors.affiliation: Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Komoda
authors.affiliation: National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
authors.forename: Mamoru
authors.initials: M
authors.lastname: Nishimoto
authors.affiliation: National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
authors.forename: Motomitsu
authors.initials: M
authors.lastname: Kitaoka
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.
authors.forename: Haruhide
authors.initials: H
authors.lastname: Mori
authors.affiliation: Graduate School of Life Science, Hokkaido University, Sapporo, Japan.|Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.|Department of Pharmacology, Basic Medical College of Zhengzhou University, Zhengzhou, China.
authors.forename: Min
authors.initials: M
authors.lastname: Yao
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008362:Mannosides / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D006005:Phosphorylases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D045857:Ruminococcus / Q000201:enzymology / Q000235:genetics; D055672:Static Electricity; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D008362:Mannosides; D006005:Phosphorylases; D006026:Glycoside Hydrolases
keywords: 4-O-β-d-mannosyl-d-glucose phosphorylase; X-ray crystallography; glycoside hydro-lase family 130; hydrogen bond-network; substrate recognition; β-1,4-mannooligosaccharide phosphorylase