title: The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1.
abstract: The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (β-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. We show that JBP1 recognizes J-containing DNA (J-DNA) through a 160-residue domain, DB-JBP1, with 10 000-fold preference over normal DNA. The crystal structure of DB-JBP1 revealed a helix-turn-helix variant fold, a 'helical bouquet' with a 'ribbon' helix encompassing the amino acids responsible for DNA binding. Mutation of a single residue (Asp525) in the ribbon helix abrogates specificity toward J-DNA. The same mutation renders JBP1 unable to rescue the targeted deletion of endogenous JBP1 genes in Leishmania and changes its distribution in the nucleus. Based on mutational analysis and hydrogen/deuterium-exchange mass-spectrometry data, a model of JBP1 bound to J-DNA was constructed and validated by small-angle X-ray scattering data. Our results open new possibilities for targeted prevention of J-DNA recognition as a therapeutic intervention for parasitic diseases.
authors.affiliation: Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Tatjana
authors.initials: T
authors.lastname: Heidebrecht
authors.forename: Evangelos
authors.initials: E
authors.lastname: Christodoulou
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Chalmers
authors.forename: Sabrina
authors.initials: S
authors.lastname: Jan
authors.forename: Bas
authors.initials: B
authors.lastname: Ter Riet
authors.forename: Rajesh K
authors.initials: RK
authors.lastname: Grover
authors.forename: Robbie P
authors.initials: RP
authors.lastname: Joosten
authors.forename: Dene
authors.initials: D
authors.lastname: Littler
authors.forename: Henri
authors.initials: H
authors.lastname: van Luenen
authors.forename: Patrick R
authors.initials: PR
authors.lastname: Griffin
authors.forename: Paul
authors.initials: P
authors.lastname: Wentworth
authors.forename: Piet
authors.initials: P
authors.lastname: Borst
authors.forename: Anastassis
authors.initials: A
authors.lastname: Perrakis
mesh_terms: D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry; D001224:Aspartic Acid / Q000737:chemistry; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004269:DNA, Bacterial / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D005960:Glucosides / Q000737:chemistry* / Q000378:metabolism; D008239:Lysine / Q000737:chemistry; D013058:Mass Spectrometry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D015800:Protozoan Proteins / Q000737:chemistry* / Q000378:metabolism; D053838:Scattering, Small Angle; D016415:Sequence Alignment; D014498:Uracil / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D014961:X-Ray Diffraction
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D005960:Glucosides; C402790:J-specific DNA-binding protein, protozoa; D015800:Protozoan Proteins; C036483:T-DNA; D001224:Aspartic Acid; C084880:5-((glucopyranosyloxy)methyl)uracil; D014498:Uracil; D004247:DNA; D001120:Arginine; D008239:Lysine