6LDM image
Entry Detail
PDB ID:
6LDM
Title:
Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1
Biological Source:
PDB Version:
Deposition Date:
2019-11-22
Release Date:
2020-03-18
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA-binding protein RAP1
Chain IDs:A
Chain Length:291
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polydeoxyribonucleotide
Description:G-guadruplex DNA
Chain IDs:B
Chain Length:19
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1.
Nucleic Acids Res. 48 4562 4571 (2020)
PMID: 32187364 DOI: 10.1093/nar/gkaa171

Abstact

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.

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