DSSR-derived G-quadruplex features in PDB entry 6ldm
Poster "DSSR-Enabled Automatic Identification and Annotation of G-quadruplexes in the PDB" presented at the RNA2020 online meeting
Citation: before a paper dedicated to the DSSR-G4 module comes out, please cite the 2015 DSSR paper published in Nucleic Acids Research.
- DNA binding protein-DNA
- X-ray (2.4 Å)
- Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein rap1
- Traczyk, A., Liew, C.W., Gill, D.J., Rhodes, D.: (2020) "Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1." Nucleic Acids Res., 48, 4562-4571.
- G-quadruplexes are four-stranded nucleic acid structures involved in multiple cellular pathways including DNA replication and telomere maintenance. Such structures are formed by G-rich DNA sequences typified by telomeric DNA repeats. Whilst there is evidence for proteins that bind and regulate G-quadruplex formation, the molecular basis for this remains poorly understood. The budding yeast telomeric protein Rap1, originally identified as a transcriptional regulator functioning by recognizing double-stranded DNA binding sites, was one of the first proteins to be discovered to also bind and promote G-quadruplex formation in vitro. Here, we present the 2.4 Å resolution crystal structure of the Rap1 DNA-binding domain in complex with a G-quadruplex. Our structure not only provides a detailed insight into the structural basis for G-quadruplex recognition by a protein, but also gives a mechanistic understanding of how the same DNA-binding domain adapts to specifically recognize different DNA structures. The key observation is the DNA-recognition helix functions in a bimodal manner: In double-stranded DNA recognition one helix face makes electrostatic interactions with the major groove of DNA, whereas in G-quadruplex recognition a different helix face is used to make primarily hydrophobic interactions with the planar face of a G-tetrad.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.078 type=planar nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15 2 glyco-bond=---- groove=---- planarity=0.155 type=planar nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16 3 glyco-bond=---- groove=---- planarity=0.225 type=bowl nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17