ISDA

Entry Detail

PDB ID:

8QPC

Keywords:

DNA BINDING PROTEIN

Title:

18mer DNA mimic Foldamer with an Aromatic linker in complex with Sac7d V26A/M29A protein

Biological Source:

Source Organism:

Sulfolobus acidocaldarius, synthetic construct

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2023-10-01

Release Date:

2023-11-08

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.24 Å

R-Value Free:

0.34

R-Value Work:

0.33

R-Value Observed:

0.33

Space Group:

P 64 2 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-binding protein 7b
Mutations:V26A/M29A
Chain IDs:A (auth: AA)
Chain Length:66
Number of Molecules:1
Biological Source:Sulfolobus acidocaldarius

UniProt ID:P13123 Pfam ID:PF02294

Polymer Type:polypeptide(L)
Description:N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide
Chain IDs:B
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polypeptide(L)
Description:N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide
Chain IDs:C
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

DNA Mimic Foldamer Recognition of a Chromosomal Protein.

Deepak, D, Wu, J, Corvaglia, V, Allmendinger, L, Scheckenbach, M, Tinnefeld, P, Huc, I, Ziach, K, Chollet, C, Parissi, V, Prabhakaran, P, Marchivie, M, Corvaglia, V, Bose, P.P, Laxmi-Reddy, K, Godde, F, Schmitter, J.M, Chaignepain, S, Pourquier, P, Huc, I, Chen, C.Y, Ko, T.P, Lin, T.W, Chou, C.C, Chen, C.J, Wang, A.H.Show

Angew.Chem.Int.Ed.Engl. 64 e202422958 e202422958 (2025)

PMID: 39714421 DOI: 10.1002/anie.202422958

Abstact

Helical aromatic oligoamide foldamers bearing anionic side chains that mimic the overall shape and charge surface distribution of DNA were synthesized. Their interactions with chromosomal protein Sac7d, a non-sequence-selective DNA-binder that kinks DNA, were investigated by Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC), Circular Dichroism spectroscopy (CD), melting curve analysis, Atomic Force Microscopy (AFM), and Nuclear Magnetic Resonance (NMR), as well as by single crystal X-ray crystallography. The foldamers were shown to bind to Sac7d better than a DNA duplex of comparable length. The interaction is diastereoselective and takes place at the DNA binding site. Crystallography revealed that the DNA mimic foldamers have a binding mode of their own and that they can bind to Sac7d without being kinked.

Legend

Protein

Chemical

Disease

Primary Citation of related structures