PDBsum entry 4xic

Transcription regulator/DNA

PDB id: 4xic

Contents

Protein chains

59 a.a.

56 a.a.

DNA/RNA

Ligands

MPD ×3

Metals

_NI ×3

Waters ×14

PDB id:

4xic

Name:

Transcription regulator/DNA

Title:

Antphd with 15bp di-thioate modified DNA duplex

Structure:

Homeotic protein antennapedia. Chain: a, d. Fragment: unp residues 297-356. Engineered: yes. DNA (5'-d( Ap Gp Ap Ap Ap Gp Cp (C2s) p Ap Tp Tp Ap Gp Ap G)-3'). Chain: b, e. Engineered: yes. DNA (5'-d( Tp Cp Tp Cp Tp Ap Ap Tp Gp Gp Cp Tp Tp Tp C)-

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: antp, cg1028. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Unidentified. Organism_taxid: 32644.

Resolution:

2.69Å R-factor: 0.219 R-free: 0.272

Authors:

M.A.White,L.Zandarashvili,J.Iwahara

Key ref:

L.Zandarashvili et al. (2015). Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate. Biophys J, 109, 1026-1037. PubMed id: 26331260 DOI: 10.1016/j.bpj.2015.07.032

Date:

06-Jan-15 Release date: 25-Nov-15

Protein chain

P02833  (ANTP_DROME) -  Homeotic protein antennapedia from Drosophila melanogaster

Seq: 378 a.a.

Struc: 59 a.a.*

Protein chain

P02833  (ANTP_DROME) -  Homeotic protein antennapedia from Drosophila melanogaster

Seq: 378 a.a.

Struc: 56 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

A-G-A-A-A-G-C-C2S-A-T-T-A-G-A-G 15 bases

T-C-T-C-T-A-A-T-G-G-C-T-T-T-C 15 bases

A-G-A-A-A-G-C-C2S-A-T-T-A-G-A-G 15 bases

T-C-T-C-T-A-A-T-G-G-C-T-T-T-C 15 bases

DOI no: 10.1016/j.bpj.2015.07.032

Biophys J 109:1026-1037 (2015)

PubMed id: 26331260

Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.

L.Zandarashvili, D.Nguyen, K.M.Anderson, M.A.White, D.G.Gorenstein, J.Iwahara.

ABSTRACT

Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3(+) groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.