title: Catalytic mechanism of aromatic prenylation by NphB.
abstract: NphB is an aromatic prenyltransferase that catalyzes the attachment of a 10-carbon geranyl group to aromatic substrates. Importantly, NphB exhibits a rich substrate selectivity and product regioselectivity. A systematic computational study has been conducted in order to address several question associated with NphB-catalyzed geranylation. The reaction mechanism of the prenylation step has been characterized as a S(N)1 type dissociative mechanism with a weakly stable carbocation intermediate. A novel π-chamber composed of Tyr121, Tyr216, and 1,6-DHN is found to be important in stabilizing the carbocation. The observed difference in the rates of product formation from 5- and 2-prenylation arises from the differing orientations of the aromatic substrate in the resting state. 4-Prenylation shares the same resting state with 5-prenylation, but the lower free energy barrier for carbocation formation makes the latter reaction more facile. The high free energy barrier associated with 7-prenylation is caused by the unfavorable orientation of 1,6-DHN in active site pocket, along with the difficulty of proton elimination after the prenylation step. A water-mediated proton transfer facilitates the loss of hydrogen at the prenylation site to form the final prenylated product. Interestingly, the same crystallographically observed water molecule has been found to be responsible for proton loss in all three experimentally identified products. After proton transfer, the relaxation of the final product from a sp(3) carbon center to a sp(2) center triggers a "spring-loaded" product release mechanism which pushes the final product out of the binding pocket toward the edge of the active site. The hydrogen bond interactions between the two hydroxyl groups of the aromatic product and the side chains of Ser214 and Tyr288 help to "steer" the movement of the product. In addition, mutagenesis studies identify these same two side chains as being responsible for the observed regioselectivity, particularly 2-prenylation. These observations provide valuable insights into NphB chemistry, offering an opportunity to better engineer the active site and to control the reactivity in order to obtain high yields of the desired product(s). Furthermore, the S(N)1 reaction mechanism observed for NphB differs from the prenylation reaction found in, for example, the farnesyltransferase, which proceeds via an S(N)2-like reaction pathway. The spring-loaded release mechanism highlighted herein also offers novel insights into how enzymes facilitate product release.
authors.affiliation: Department of Chemistry and the Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, United States.
authors.forename: Yue
authors.initials: Y
authors.lastname: Yang
authors.forename: Yipu
authors.initials: Y
authors.lastname: Miao
authors.forename: Bing
authors.initials: B
authors.lastname: Wang
authors.forename: Guanglei
authors.initials: G
authors.lastname: Cui
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Merz
mesh_terms: D055162:Biocatalysis; D004122:Dimethylallyltranstransferase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011756:Diphosphates / Q000378:metabolism; D004224:Diterpenes / Q000378:metabolism; D051231:Farnesyltranstransferase / Q000378:metabolism; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009284:Naphthols / Q000737:chemistry / Q000378:metabolism; D017354:Point Mutation; D011487:Protein Conformation; D017368:Protein Prenylation; D011522:Protons; D011789:Quantum Theory; D013302:Streptomyces / Q000201:enzymology; D013379:Substrate Specificity
chemical_list: D011756:Diphosphates; D004224:Diterpenes; D009284:Naphthols; D011522:Protons; C511282:geranyl diphosphate; D004122:Dimethylallyltranstransferase; D051231:Farnesyltranstransferase