2LWN | pdb_00002lwn

Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion

• PDB DOI: https://doi.org/10.2210/pdb2LWN/pdb
• NAKB: 2LWN
• BMRB: 18639

• Classification: DNA
• Mutation(s): No 


• Deposited: 2012-08-03 Released: 2013-02-20 
• Deposition Author(s): Zalianyak, T., de los Santos, C., Lukin, M., Attaluri, S., Johnson, F.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 19 
• Conformers Submitted: 20 
• Selection Criteria: all calculated structures submitted 

Literature

Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion

Lukin, M., Zaliznyak, T., Attaluri, S., Johnson, F., de Los Santos, C.

(2012) Chem Res Toxicol 25: 2423-2431

• PubMed: 22897814 
• DOI: https://doi.org/10.1021/tx300290b
• Primary Citation Related Structures: 
  2LWM, 2LWN, 2LWO


• PubMed Abstract: 
  

  The addition of hydroxyl radicals to the C8 position of guanine can lead to the formation of a 2,6-diamino-4-hydroxy-5-formamido-2'-deoxypyrimidine (Fapy-dG) lesion, whose endogenous levels in cellular DNA rival those of 8-oxo-7,8-dihydroxy-2'-deoxyguanosine. Despite its prevalence, the structure of duplex DNA containing Fapy-dG is unknown. We have prepared an undecameric duplex containing a centrally located β-cFapy-dG residue paired to dC and determined its solution structure by high-resolution NMR spectroscopy and restrained molecular dynamic simulations. The damaged duplex adopts a right-handed helical structure with all residues in an anti conformation, forming Watson-Crick base pair alignments, and 2-deoxyribose conformations in the C2'-endo/C1'-exo range. The formamido group of Fapy rotates out of the pyrimidine plane and is present in the Z and E configurations that equilibrate with an approximate 2:1 population ratio. The two isomeric duplexes show similar lesion-induced deviations from a canonical B-from DNA conformation that are minor and limited to the central three-base-pair segment of the duplex, affecting the stacking interactions with the 5-lesion-neighboring residue. We discuss the implications of our observations for translesion synthesis during DNA replication and the recognition of Fapy-dG by DNA glycosylases.

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Organizational Affiliation: 
• Department of Pharmacological Sciences, Stony Brook University-School of Medicine, Stony Brook, NY 11794-8651, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.72 kDa 
• Atom Count: 446 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*AP*C*(LWM)P*CP*AP*TP*GP*C)-3')	A [auth B]	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3')	B [auth D]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 19 
• Conformers Submitted: 20 
• Selection Criteria: all calculated structures submitted 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Zalianyak, T., de los Santos, C., Lukin, M., Attaluri, S., Johnson, F.

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations