2KV6

Tetrapeptide KWKK conjugated to oligonucleotide duplex by a trimethylene tether

Summary for 2KV6

• Entry DOI: 10.2210/pdb2kv6/pdb
• Descriptor: 5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3', 5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3', KWKK Tetrapeptide (3 entities in total)
• Functional Keywords: dna-peptide conjugate, trimethylene, acrolein-dg adduct, dna-peptide complex, dna binding protein-dna complex, dna binding protein/dna
• Total number of polymer chains: 3
• Total formula weight: 7960.63

Authors

Huang, H.,Kozekov, I.D.,Kozekova, A.,Rizzo, C.J.,McCullough, A.,LLoyd, R.S.,Stone, M.P. (deposition date: 2010-03-08, release date: 2010-07-21, Last modification date: 2024-10-16)

Primary citation

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

PubMed 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.

PubMed: 20604523
DOI: 10.1021/bi100364f

Experimental method

SOLUTION NMR