6LDM

Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1

Summary for 6LDM

• Entry DOI: 10.2210/pdb6ldm/pdb
• Descriptor: DNA-binding protein RAP1, G-guadruplex DNA, GLYCEROL, ... (7 entities in total)
• Functional Keywords: complex, g-quadruplex, dna, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 2
• Total formula weight: 40346.04

Authors

Traczyk, A.,Gill, D.J.,Chong, W.L.,Rhodes, D. (deposition date: 2019-11-22, release date: 2020-03-18, Last modification date: 2023-11-22)

Primary citation

Traczyk, A.,Liew, C.W.,Gill, D.J.,Rhodes, D.
Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1.
Nucleic Acids Res., 48:4562-4571, 2020

PubMed Abstract: 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.

PubMed: 32187364
DOI: 10.1093/nar/gkaa171

Experimental method

X-RAY DIFFRACTION (2.4 Å)