Structural basis for 5′-end-specific recognition of single-stranded DNA by the R3H domain from human Sμbp-2

Jaudzems, Kristaps, Jia, Xinying, Yagi, Hiromasa, Zhulenkovs, Dmitry, Graham, Bim, Otting, Gottfried and Liepinsh, Edvards (2012) Structural basis for 5′-end-specific recognition of single-stranded DNA by the R3H domain from human Sμbp-2. Journal of Molecular Biology, 424 1-2: 42-53. doi:10.1016/j.jmb.2012.09.010


Author Jaudzems, Kristaps
Jia, Xinying
Yagi, Hiromasa
Zhulenkovs, Dmitry
Graham, Bim
Otting, Gottfried
Liepinsh, Edvards
Title Structural basis for 5′-end-specific recognition of single-stranded DNA by the R3H domain from human Sμbp-2
Journal name Journal of Molecular Biology   Check publisher's open access policy
ISSN 0022-2836
1089-8638
Publication date 2012-11-23
Year available 2012
Sub-type Article (original research)
DOI 10.1016/j.jmb.2012.09.010
Open Access Status Not yet assessed
Volume 424
Issue 1-2
Start page 42
End page 53
Total pages 12
Place of publication London, United Kingdom
Publisher Academic Press
Language eng
Formatted 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.
Keyword NMR spectroscopy
Nucleotide binding
Pseudocontact shifts
R3H domain
Sμbp-2
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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