title: Structural basis for 5'-end-specific recognition of single-stranded DNA by the R3H domain from human Sμbp-2.
abstract: The R3H domain is a conserved sequence motif in nucleic acid binding proteins. Previously, we reported the solution structure of the R3H domain and identified a putative nucleic acid binding site composed of three conserved basic residues [Liepinsh, E., Leonchiks, A., Sharipo, A., Guignard, L. & Otting, G. (2003). Solution structure of the R3H domain from human Sμbp-2. J. Mol. Biol.326, 217-223]. Here, we determine the binding affinities of mononucleotides and dinucleotides for the R3H domain from human Sμbp-2 (Sμbp2-R3H) and map their binding sites on the protein's surface. Although the binding affinities show up to 260-fold selectivity between different nucleotides, their binding sites and conformations seem very similar. Further, we report the NMR structure of the Sμbp2-R3H in complex with deoxyguanosine 5'-monophosphate (dGMP) mimicking the 5'-end of single-stranded DNA. Pseudocontact shifts from a paramagnetic lanthanide tag attached to residue 731 in the mutant A731C confirmed that binding of dGMP brings a loop of the protein into closer proximity. The structure provides the first structural insight into single-stranded nucleic acid recognition by the R3H domain and shows that the R3H domain specifically binds the phosphorylated 5'-end through electrostatic interactions with the two conserved arginines and stacking interactions with the highly conserved histidine.
authors.affiliation: Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Latvia. kristaps.jaudzems@osi.lv
authors.forename: Kristaps
authors.initials: K
authors.lastname: Jaudzems
authors.forename: Xinying
authors.initials: X
authors.lastname: Jia
authors.forename: Hiromasa
authors.initials: H
authors.lastname: Yagi
authors.forename: Dmitry
authors.initials: D
authors.lastname: Zhulenkovs
authors.forename: Bim
authors.initials: B
authors.lastname: Graham
authors.forename: Gottfried
authors.initials: G
authors.lastname: Otting
authors.forename: Edvards
authors.initials: E
authors.lastname: Liepinsh
mesh_terms: D001665:Binding Sites; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; C489892:IGHMBP2 protein, human; D014157:Transcription Factors