title: Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences.
abstract: Norovirus (NV) RNA-dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer-template duplex was investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the post-incorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435-1445. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Division of Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, 02115.|Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, Massachusetts, 02115.
authors.forename: Md Munan
authors.initials: MM
authors.lastname: Shaik
authors.affiliation: Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France.
authors.forename: Nicholus
authors.initials: N
authors.lastname: Bhattacharjee
authors.affiliation: Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France.
authors.forename: Mikolaj
authors.initials: M
authors.lastname: Feliks
authors.affiliation: Department of Biological Sciences and Alberta Glycomics Centre, University of Calgary, Calgary, Alberta, Canada.
authors.forename: Kenneth K-S
authors.initials: KK
authors.lastname: Ng
authors.affiliation: Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France.
authors.forename: Martin J
authors.identifier: http://orcid.org/0000-0001-8674-7997
authors.initials: MJ
authors.lastname: Field
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D020134:Catalytic Domain; D002413:Cations, Divalent; D003035:Cobalt / Q000737:chemistry; D003300:Copper / Q000737:chemistry*; D018360:Crystallography, X-Ray; D007501:Iron / Q000737:chemistry; D007700:Kinetics; D008345:Manganese / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009532:Nickel / Q000737:chemistry; D029322:Norovirus / Q000737:chemistry* / Q000201:enzymology; D009843:Oligoribonucleotides / Q000737:chemistry*; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D011789:Quantum Theory; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D013816:Thermodynamics; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015032:Zinc / Q000737:chemistry
chemical_list: D002413:Cations, Divalent; D009843:Oligoribonucleotides; D011994:Recombinant Proteins; D014764:Viral Proteins; D003035:Cobalt; D008345:Manganese; D003300:Copper; D009532:Nickel; D007501:Iron; D012324:RNA-Dependent RNA Polymerase; D015032:Zinc
keywords: RNA-dependent RNA polymerase; gastroenteritis; metal binding; norovirus; quantum chemical/molecular mechanical hybrid potentials