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PDBsum entry 2oiy

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dna_rna metals links
RNA PDB id
2oiy
Jmol
Contents
DNA/RNA
Metals
_MG ×2
__K ×3
Waters ×183
PDB id:
2oiy
Name: RNA
Title: Crystal structure of the duplex form of the HIV-1(lai) RNA dimerization initiation site
Structure: 5'-r( Cp Up Up Gp Cp Up Gp Ap Ap Gp Cp Gp Cp Gp C Gp Cp Ap Ap G)-3'. Chain: a, b. Engineered: yes. Other_details: HIV-1subtype b dis RNA, dimerization initiat
Source: Synthetic: yes. Other_details: HIV-1 genomic RNA lai isolate (HIV-1 subtype
Resolution:
1.60Å     R-factor:   0.242     R-free:   0.250
Authors: E.Ennifar,P.Walter,P.Dumas
Key ref: E.Ennifar et al. (2010). Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site. Nucleic Acids Res, 38, 5807-5816. PubMed id: 20460458
Date:
12-Jan-07     Release date:   25-Dec-07    
 Headers
 References

 

 
Nucleic Acids Res 38:5807-5816 (2010)
PubMed id: 20460458  
 
 
Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site.
E.Ennifar, P.Walter, P.Dumas.
 
  ABSTRACT  
 
The crystal structure of subtype-B HIV-1 genomic RNA Dimerization Initiation Site duplex revealed chain cleavage at a specific position resulting in 3'-phosphate and 5'-hydroxyl termini. A crystallographic analysis showed that Ba(2+), Mn(2+), Co(2+) and Zn(2+) bind specifically on a guanine base close to the cleaved position. The crystal structures also point to a necessary conformational change to induce an 'in-line' geometry at the cleavage site. In solution, divalent cations increased the rate of cleavage with pH/pKa compensation, indicating that a cation-bound hydroxide anion is responsible for the cleavage. We propose a 'Trojan horse' mechanism, possibly of general interest, wherein a doubly charged cation hosted near the cleavage site as a 'harmless' species is further transformed in situ into an 'aggressive' species carrying a hydroxide anion.