title: Identification of a potential proton donor to the linking oxygen atom in a three-metal ion assisted catalysis pathway catalyzed by Fructose-1, 6-bisphosphatase.
abstract: In this paper, the dephosphorylation mechanism of FBP to F6P catalyzed by the Fructose-1, 6-bisphosphatase (St-Fbp) from Sulfolobus tokodaii was studied using quantum mechanical/molecular mechanical (QM/MM) approach. Based on the experimental results, total five possible catalytic mechanisms (path1-path4') were designed. The most possible dephosphorylation reaction follows a two-step mechanism (path2): a dephosphorylation process (with D12 being an base of W6 and residue K133 being the proton donor of the linking FBP:O4) and a proton exchange process (between K133 and the water W1). Furthermore, the three-step of path4 is also possible: a dephosphorylation process (with D54 being the base of W6 and residue K133 being the proton donor of the linking FBP:O4) and two proton exchange processes (first between residues D54 and D12 then between K133 and the water W1). The relative low energy of this pathway suggests that D54 might also be a base except D12. Our calculations indicate that K133 is the preferred proton donor during the breaking of the phosphate bond O4-P1, with the W1 being an alternative proton donor to access to a more stable product. Findings here give a new insight into the understanding of catalytic mechanism of FBPase.
authors.affiliation: College of Chemistry, Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, China. Electronic address: jinhuwang_07@mail.sdu.edu.cn.
authors.forename: Jinhu
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China. Electronic address: zhgwang@aliyun.com.
authors.forename: Zhiguo
authors.initials: Z
authors.lastname: Wang
authors.affiliation: College of Chemistry Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, China.
authors.forename: Baoping
authors.initials: B
authors.lastname: Ling
authors.affiliation: College of Chemistry, Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Cao
authors.affiliation: College of Chemistry, Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
mesh_terms: D001665:Binding Sites; D055162:Biocatalysis; D018360:Crystallography, X-Ray; D006597:Fructose-Bisphosphatase / Q000737:chemistry / Q000378:metabolism*; D007477:Ions; D008670:Metals / Q000378:metabolism*; D008958:Models, Molecular; D010100:Oxygen / Q000378:metabolism*; D010766:Phosphorylation; D011522:Protons; D011789:Quantum Theory; D016944:Sulfolobus / Q000201:enzymology*; D013816:Thermodynamics
chemical_list: D007477:Ions; D008670:Metals; D011522:Protons; D006597:Fructose-Bisphosphatase; D010100:Oxygen
keywords: Dephosphorylation; Nucleophilic; Proton donor; Quantum mechanical/molecular mechanical (QM/MM); d-Fructose-1,6-bisphosphate (FBP)