6LFF

transcription factor SATB1 CUTr1 domain in complex with a phosphorothioate DNA

Summary for 6LFF

• Entry DOI: 10.2210/pdb6lff/pdb
• Related: 2O49 2O4A
• Descriptor: DNA-binding protein SATB1, DNA (5'-D(*GP*(C7R)P*(PST)P*AP*AP*TP*AP*TP*AP*TP*GP*C)-3'), DNA (5'-D(*GP*CP*AP*TP*(AS)P*(PST)P*(AS)P*(PST)P*TP*AP*GP*C)-3'), ... (4 entities in total)
• Functional Keywords: dna-binding protein, dna modification, transcription factor, transcription, transcription-dna complex, transcription/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 29323.99

Authors

Akutsu, Y.,Kubota, T.,Yamasaki, T.,Yamasaki, K. (deposition date: 2019-12-02, release date: 2020-04-01, Last modification date: 2023-11-22)

Primary citation

Yamasaki, K.,Akutsu, Y.,Yamasaki, T.,Miyagishi, M.,Kubota, T.
Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts.
Nucleic Acids Res., 48:4551-4561, 2020

PubMed Abstract: Phosphorothioate modification is commonly introduced into therapeutic oligonucleotides, typically as a racemic mixture in which either of the two non-bridging phosphate oxygens is replaced by sulfur, which frequently increases affinities with proteins. Here, we used isothermal titration calorimetry and X-ray crystallography to investigate the thermodynamic and structural properties of the interaction between the primary DNA-binding domain (CUTr1) of transcription factor SATB1 and dodecamer DNAs with racemic phosphorothioate modifications at the six sites known to contact CUTr1 directly. For both the modified and unmodified DNAs, the binding reactions were enthalpy-driven at a moderate salt concentration (50 mM NaCl), while being entropy-driven at higher salt concentrations with reduced affinities. The phosphorothioate modifications lowered this susceptibility to salt, resulting in a significantly enhanced affinity at a higher salt concentration (200 mM NaCl), although only some DNA molecular species remained interacting with CUTr1. This was explained by unequal populations of the two diastereomers in the crystal structure of the complex of CUTr1 and the phosphorothioate-modified DNA. The preferred diastereomer formed more hydrogen bonds with the oxygen atoms and/or more hydrophobic contacts with the sulfur atoms than the other, revealing the origins of the enhanced affinity.

PubMed: 32187371
DOI: 10.1093/nar/gkaa170

Experimental method

X-RAY DIFFRACTION (1.79 Å)