PDBsum entry 2kv6

DNA binding protein/DNA

PDB id: 2kv6

Contents

DNA/RNA

Ligands

LYS-TRP-LYS-LYS

PDB id:

2kv6

Name:

DNA binding protein/DNA

Title:

Tetrapeptide kwkk conjugated to oligonucleotide duplex by a trimethylene tether

Structure:

5'-d( Gp Cp Tp Ap Gp Cp Gp Ap Gp Tp Cp C)-3'. Chain: a. Engineered: yes. 5'-d( Gp Gp Ap Cp Tp Cp Gp Cp Tp Ap Gp C)-3'. Chain: b. Engineered: yes. Kwkk tetrapeptide. Chain: c. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

1 models

Authors:

H.Huang,I.D.Kozekov,A.Kozekova,C.J.Rizzo,A.Mccullough,R.S.Lloyd, M.P.Stone

Key ref:

H.Huang et al. (2010). Minor groove orientation of the KWKK peptide tethered via the N-terminal amine to the acrolein-derived 1,N2-gamma-hydroxypropanodeoxyguanosine lesion with a trimethylene linkage. Biochemistry, 49, 6155-6164. PubMed id: 20604523

Date:

08-Mar-10 Release date: 21-Jul-10

DNA/RNA chains

G-C-T-A-G-C-0AD-A-G-T-C-C 12 bases

G-G-A-C-T-C-G-C-T-A-G-C 12 bases

Biochemistry 49:6155-6164 (2010)

PubMed id: 20604523

Minor groove orientation of the KWKK peptide tethered via the N-terminal amine to the acrolein-derived 1,N2-gamma-hydroxypropanodeoxyguanosine lesion with a trimethylene linkage.

H.Huang, I.D.Kozekov, A.Kozekova, C.J.Rizzo, A.K.McCullough, R.S.Lloyd, M.P.Stone.

ABSTRACT

DNA-protein conjugates are potentially repaired via proteolytic digestion to DNA-peptide conjugates. The latter have been modeled with the amino-terminal lysine of the peptide KWKK conjugated via a trimethylene linkage to the N(2)-dG amine positioned in 5'-d(GCTAGCXAGTCC)-3'.5'-d(GGACTCGCTAGC)-3' (X = N(2)-dG-trimethylene link-KWKK). This linkage is a surrogate for the reversible linkage formed by the gamma-OH-1,N(2)-propanodeoxyguanosine (gamma-OH-PdG) adduct. This conjugated KWKK stabilizes the DNA. Amino acids K(26), W(27), K(28), and K(29) are in the minor groove. The W(27) indolyl group does not intercalate into the DNA. The G(7) N(2) amine and the K(26) N-terminal amine nitrogens are in the trans configuration with respect to the C(alpha) or C(gamma) of the trimethylene tether, respectively. The structure of this DNA-KWKK conjugate is discussed in the context of its biological processing.