title: Analysis of decapping scavenger cap complex using modified cap analogs reveals molecular determinants for efficient cap binding.
abstract: Decapping scavenger (DcpS) assists in precluding inhibition of cap-binding proteins by hydrolyzing cap species remaining after mRNA 3'→5' degradation. Its significance was reported in splicing, translation initiation and microRNA turnover. Here we examine the structure and binding mode of DcpS from Caenorhabditis elegans (CeDcpS) using a large collection of chemically modified methylenebis(phosphonate), imidodiphosphate and phosphorothioate cap analogs. We determine that CeDcpS is a homodimer and propose high accuracy structural models of apo- and m(7) GpppG-bound forms. The analysis of CeDcpS regioselectivity uncovers that the only site of hydrolysis is located between the β and γ phosphates. Structure-affinity relationship studies of cap analogs for CeDcpS reveal molecular determinants for efficient cap binding: a strong dependence on the type of substituents in the phosphate chain, and reduced binding affinity for either methylated hydroxyl groups of m(7) Guo or an extended triphosphate chain. Docking analysis of cap analogs in the CeDcpS active site explains how both phosphate chain mobility and the orientation in the cap-binding pocket depend on the number of phosphate groups, the substituent type and the presence of the second nucleoside. Finally, the comparison of CeDcpS with its well known human homolog provides general insights into DcpS-cap interactions.
authors.affiliation: Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Wypijewska del Nogal
authors.forename: Marius D
authors.initials: MD
authors.lastname: Surleac
authors.forename: Joanna
authors.initials: J
authors.lastname: Kowalska
authors.forename: Maciej
authors.initials: M
authors.lastname: Lukaszewicz
authors.forename: Jacek
authors.initials: J
authors.lastname: Jemielity
authors.forename: Martin
authors.initials: M
authors.lastname: Bisaillon
authors.forename: Edward
authors.initials: E
authors.lastname: Darzynkiewicz
authors.forename: Adina L
authors.initials: AL
authors.lastname: Milac
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Bojarska
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism*; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020134:Catalytic Domain; D002850:Chromatography, Gel; D002851:Chromatography, High Pressure Liquid; D005786:Gene Expression Regulation; D006801:Humans; D006868:Hydrolysis; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011755:Pyrophosphatases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012314:RNA Cap Analogs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012315:RNA Caps / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*
chemical_list: D029742:Caenorhabditis elegans Proteins; D012314:RNA Cap Analogs; D012315:RNA Caps; D012333:RNA, Messenger; D011755:Pyrophosphatases; C509343:dcs-1 protein, C elegans
keywords: cap analogs; fluorescence spectroscopy; mRNA degradation; molecular docking; scavenger decapping enzymes