2KV6 image
Deposition Date 2010-03-08
Release Date 2010-07-21
Last Version Date 2024-10-16
Entry Detail
PDB ID:
2KV6
Keywords:
DNA BINDING PROTEIN/DNA
Title:
Tetrapeptide KWKK conjugated to oligonucleotide duplex by a trimethylene tether
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
10
Conformers Submitted:
1
Selection Criteria:
back calculated data agree with experimental NOESY spectrum
2KV6 validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'
Chain IDs:A
Chain Length:12
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3'
Chain IDs:B
Chain Length:12
Number of Molecules:1
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0AD A DG ?
Ligand Molecules
NA
Primary Citation
Minor Groove Orientation of the KWKK Peptide Tethered via the N-Terminal Amine to the Acrolein-Derived 1,N(2)-gamma-Hydroxypropanodeoxyguanosine Lesion with a Trimethylene Linkage .
Biochemistry 49 6155 6164 (2010)
PMID: 20604523 DOI: 10.1021/bi100364f

Abstact

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.

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Primary Citation of related structures
2KV6