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protein dna_rna metals links
Viral protein/DNA PDB id
2jzw
Jmol
Contents
Protein chain
44 a.a. *
DNA/RNA
Metals
_ZN ×2
* Residue conservation analysis
PDB id:
2jzw
Name: Viral protein/DNA
Title: How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription
Structure: HIV-1 nucleocapsid protein ncp7(12-55). Chain: a. Engineered: yes. DNA (5'- d( Dgp Dtp Dcp Dcp Dcp Dtp Dgp Dtp Dtp Dcp Dgp Dgp Dgp Dc)- 3'). Chain: b. Engineered: yes. Other_details: HIV-1 primer binding site pbs
Source: Synthetic: yes. Synthetic: yes
NMR struc: 19 models
Authors: S.Bourbigot,N.Ramalanjaona,G.F.J.Salgado,Y.Mely,B.P.Roques, S.Bouaziz,N.Morellet
Key ref:
S.Bourbigot et al. (2008). How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription. J Mol Biol, 383, 1112-1128. PubMed id: 18773912 DOI: 10.1016/j.jmb.2008.08.046
Date:
21-Jan-08     Release date:   13-Jan-09    
PROCHECK
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 Headers
 References

 

 
DOI no: 10.1016/j.jmb.2008.08.046 J Mol Biol 383:1112-1128 (2008)
PubMed id: 18773912  
 
 
How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription.
S.Bourbigot, N.Ramalanjaona, C.Boudier, G.F.Salgado, B.P.Roques, Y.Mély, S.Bouaziz, N.Morellet.
 
  ABSTRACT  
 
The human immunodeficiency virus type 1 nucleocapsid protein (NCp7) plays an important role in the second strand transfer during reverse transcription. It promotes annealing of the 18-nucleotide complementary DNA primer-binding site (PBS) sequences at the 3' ends of (-)DNA and (+)DNA. NMR studies show that NCp7(12-55) and NCp7(1-55) interact at the 5' end of the loop of DeltaP(-)PBS, a (-)PBS derivative without the 3' protruding sequence, in a slow-exchange equilibrium. This interaction is mediated through the binding of the hydrophobic plateau (Val13, Phe16, Thr24, Ala25, Trp37, and Met46) on the zinc finger domain of both peptides to the 5-CTG-7 sequence of DeltaP(-)PBS. The stacking of the Trp37 aromatic ring with the G7 residue likely constitutes the determinant factor of the interaction. Although NCp7(12-55) does not melt the DeltaP(-)PBS stem-loop structure, it opens the loop and weakens the C5.G11 base pair next to the loop. Moreover, NCp7(12-55) was also found to bind but with lower affinity to the 10-CGG-12 sequence in an intermediate-exchange equilibrium on the NMR time scale. The loop modifications may favour a kissing interaction with the complementary (+)PBS loop. Moreover, the weakening of the upper base pair of the stem likely promotes the melting of the stem that is required to convert the kissing complex into the final (+/-)PBS extended duplex.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Protein and oligonucleotide sequences used in this study: (a) NCp7(1–55), (b) (−)PBS, and (c) ΔP(−)PBS. (d) Model for the kissing complex homodimer. 		Figure 3.
Fig. 3. Comparison of the ΔP(−)PBS structure (a) in its free form and (b) complexed with NCp7(12–55). The heavy atoms of the stem were superimposed: C3 to C5 and G11 to G13 (in blue). T2 is in orange, G1 and C14 are in yellow, and bases from the loop are in light green, except T6 and G7, which are in dark green.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 383, 1112-1128) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21227929 A.Bazzi, L.Zargarian, F.Chaminade, C.Boudier, H.De Rocquigny, B.René, Y.Mély, P.Fossé, and O.Mauffret (2011).
Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC.
  Nucleic Acids Res, 39, 3903-3916.  
21253649 S.M.Quintal, Q.A.dePaula, and N.P.Farrell (2011).
Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences.
  Metallomics, 3, 121-139.  
20213668 R.J.Falconer, A.Penkova, I.Jelesarov, and B.M.Collins (2010).
Survey of the year 2008: applications of isothermal titration calorimetry.
  J Mol Recognit, 23, 395-413.  
19357935 P.Mendoza-Espinosa, V.García-González, A.Moreno, R.Castillo, and J.Mas-Oliva (2009).
Disorder-to-order conformational transitions in protein structure and its relationship to disease.
  Mol Cell Biochem, 330, 105-120.  
19151084 V.V.Shvadchak, A.S.Klymchenko, H.de Rocquigny, and Y.Mély (2009).
Sensing peptide-oligonucleotide interactions by a two-color fluorescence label: application to the HIV-1 nucleocapsid protein.
  Nucleic Acids Res, 37, e25.  
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