Primary Citation PubMed: 19877603
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De novo polymerase activity and oligomerization of hepatitis C virus RNA-dependent RNA-polymerases from genotypes 1 to 5.
(2011) PLoS One 6
PubMed: 21490973 | PubMedCentral: PMC3072391 | DOI: 10.1371/journal.pone.0018515
A number of crystal structures of the HCV polymerase (i.e. 1GX5, 1NHU, 1NHV, 1OS5, 1YVZ, 2BRL, 2D3U, 2D3Z, 2D41, 2DXS, 2GIR, 2HAI, 2HWH, 2HWI, 2I1R, 2JC0, 2O5D, 2WCX, 2WHO, 3CJ0, 3CJ2, 3CJ3, 3CJ4, 3CJ... , 3FRZ and 3HVO), show that the αT helix is close to a site of interaction for non-nucleoside inhibitors.
Publication Year: 2011
Evidence for a non-catalytic ion-binding site in multiple RNA-dependent RNA polymerases.
(2012) PLoS One 7
PubMed: 22792374 | PubMedCentral: PMC3394715 | DOI: 10.1371/journal.pone.0040581
The pseudomonas phage φ6 RdRp structure (PDBid: 1HHS) was used as a reference for the position of the non-catalytic ion ( Fig. 1C ), and the RdRp structure of the hepatitis C virus (PDBid: 2WH... ) was used as a reference for the positions of the catalytic ions ( Fig. 1B ).
In several RdRp structures, the observed catalytic ions were clearly shifted from the locations that they occupied in the RdRp structure of the hepatitis C virus (PDBid: 2WHO) (which, in this study, was used as a reference for defining the catalytic position; Fig. 1B ) towards the thumb subdomain (e.g., compare Fig. 2B , panels VIIII and II).
(A) Conserved motifs in the phage φ6 RdRp (PDBid: 1HHS) and magnified views of the catalytic sites from the RdRps of hepatitis C virus (B) and phage φ6 (C) (PDBids: 2WHO and 1HHS, respectively).
Measurements of the Distances between the Non-catalytic and Catalytic Ions The distances between the non-catalytic and catalytic ions were determined by structurally aligning each non-catalytic ion containing vRdRp with the RdRp of the hepatitis C virus (PDBid: 2WHO) containing the catalytic ions ( Fig. 1B ).
Although diffuse, the cluster of ions at the catalytic site was clearly bipartite, reflecting the distinct positions of catalytic ions A and B. Distances between the Catalytic and Non-catalytic Ions To obtain comparable distance measurements for the observed non-catalytic ions from the catalytic site, the representative vRdRp structures from all the viral species identified in Table 2 were superimposed on the structure of the hepatitis C virus RdRp containing catalytic ions (PDBid: 2WHO).
5 Structures were structurally aligned with the hepatitis C virus RdRp structure (PDBid: 2WHO).
Publication Year: 2012
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