8IPF

Crystal structure of an ankyrin protein that can specifically recognize a parallel G-quadruplex

Summary for 8IPF

• Entry DOI: 10.2210/pdb8ipf/pdb
• Related: 8IPP
• Descriptor: DARPin (2E4) (2 entities in total)
• Functional Keywords: g-quadruplex, parallel, dna, dna binding protein
• Biological source: synthetic construct
• Total number of polymer chains: 8
• Total formula weight: 118917.54

Authors

Ngo, K.H.,Liew, C.W.,Heddi, B.,Phan, A.T. (deposition date: 2023-03-14, release date: 2024-07-31)

Primary citation

Ngo, K.H.,Liew, C.W.,Heddi, B.,Phan, A.T.
Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein.
J.Am.Chem.Soc., 146:13709-13713, 2024

PubMed Abstract: G-Quadruplex (G4) structures formed by guanine-rich DNA and RNA sequences are implicated in various biological processes. Understanding the mechanisms by which proteins recognize G4 structures is crucial for elucidating their functional roles. Here we present the X-ray crystal structure of an ankyrin protein bound to a parallel G4 structure. Our findings reveal a new specific recognition mode in which a bundle of α-helices and loops of the ankyrin form a flat surface to stack on the G-tetrad core. The protein employs a combination of hydrogen bonds and hydrophobic contacts to interact with the G4, and electrostatic interaction is used to enhance the binding affinity. This binding mechanism provides valuable insights into understanding G4 recognition by proteins.

PubMed: 38738955
DOI: 10.1021/jacs.4c01971

Experimental method

X-RAY DIFFRACTION (2.01 Å)