2KV6 | pdb_00002kv6

Tetrapeptide KWKK conjugated to oligonucleotide duplex by a trimethylene tether

• PDB DOI: https://doi.org/10.2210/pdb2KV6/pdb
• NAKB: 2KV6

• Classification: DNA BINDING PROTEIN/DNA
• Mutation(s): No 


• Deposited: 2010-03-08 Released: 2010-07-21 
• Deposition Author(s): Huang, H., Kozekov, I.D., Kozekova, A., Rizzo, C.J., McCullough, A., LLoyd, R.S., Stone, M.P.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 1 
• Selection Criteria: back calculated data agree with experimental NOESY spectrum 

Literature

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 .

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

(2010) Biochemistry 49: 6155-6164

• PubMed: 20604523 
• DOI: https://doi.org/10.1021/bi100364f
• Primary Citation Related Structures: 
  2KV6


• 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.

---

Organizational Affiliation: 
• Department of Chemistry, Center in Molecular Toxicology, Center for Structural Biology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.96 kDa 
• Atom Count: 531 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
KWKK Tetrapeptide	C	4	N/A	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'	A	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3'	B	12	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 1 
• Selection Criteria: back calculated data agree with experimental NOESY spectrum 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Huang, H., Kozekov, I.D., Kozekova, A., Rizzo, C.J., McCullough, A., LLoyd, R.S., Stone, M.P.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary