NS5B

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<applet load='2HAI_catalytic3.pdb' size='400' frame='true' align='right' caption='Figure 3.' />
<applet load='2HAI_catalytic3.pdb' size='400' frame='true' align='right' caption='Figure 3.' />
'''Figure 3''' explores empirically determined sites of protein-ssRNA interactions. The highlighted <scene name='NS5B/Ns5b_rna_interactions/1'>peptide segments</scene> were each identified without x-ray crystallography or NMR. These RNA binding peptides were identified by cross linking single stranded RNA to NS5B followed by a tryptic digest of the protein, then purification of the RNA bound peptide segments by affinity (for the RNA) chromatography. The segments of peptide that stuck to the column meaning they had been cross linked to RNA were then analyzed with MALDI mass spectrometry. It is interesting that all of the contacts were in the <scene name='NS5B/Native_ns5b/3'>fingers domain.</scene> This could be in part due to the fact that single stranded RNA was cross linked to the enzyme, the fingers domain is thought to bind templating ssRNA while other regions of the polymerase would bind duplex RNA.
'''Figure 3''' explores empirically determined sites of protein-ssRNA interactions. The highlighted <scene name='NS5B/Ns5b_rna_interactions/1'>peptide segments</scene> were each identified without x-ray crystallography or NMR. These RNA binding peptides were identified by cross linking single stranded RNA to NS5B followed by a tryptic digest of the protein, then purification of the RNA bound peptide segments by affinity (for the RNA) chromatography. The segments of peptide that stuck to the column meaning they had been cross linked to RNA were then analyzed with MALDI mass spectrometry. It is interesting that all of the contacts were in the <scene name='NS5B/Native_ns5b/3'>fingers domain.</scene> This could be in part due to the fact that single stranded RNA was cross linked to the enzyme, the fingers domain is thought to bind templating ssRNA while other regions of the polymerase would bind duplex RNA.
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Revision as of 14:26, 21 April 2009

RNA Dependent RNA Polymerase from Hepatitis C Virus

Figure 1. PDB ID 2HAI

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NS5B is the RNA dependent RNA polymerase of Hepatitis C virus. NS5B, like other RNA dependent RNA polymerases, is error prone. This viral RNA replicase is of approximately a million times lower fidelity than a replicative prokayrotic or eukaryotic DNA polymerase. This is due in part to the fact that NS5B contains no exonuclease or proofreading domain. The proposed mechanism for NS5B polymerization of monomers of RNA triphosphates to extend a primer strand, that may have initiated de novo, is via two divalent cations coordinated by carboxyl groups as seen in DNA polymerases. In the case of NS5B the residues that coordinate divalent cations (Mg2+ or Mn2+ in vitro) are the three

seen here.

Though Hepatitis C virus is of the Flaviviridae family the structure of NS5B is similar to the polymerase of bacteriophage Φ 6. The similarity to the bacteriophage polymerase is due to NS5B containing a fully encircled active site. Like many template-dependent nucleotide polymerases, NS5B can be visualized similar to a right hand. NS5B contains several , fingers in blue, palm in magenta, thumb in green and a c-terminal domain in yellow. The palm domain contains the active site aspartates and there are several contacts between the fingers and thumbs domain that give the active site an encircled structure. There is a that is proposed to move upon formation of exiting double stranded RNA.

Figure 2. PDB IDs 2HAI (protein) 1RTD (DNA)

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Figure 2 is a model of NS5B with B form DNA. DNA was modeled into the NS5B model by aligning of palm domain of NS5B and the palm domain of HIV reverse transcriptase, which was co-crystallized in complex with DNA and an incoming dTTP. Then removing the protein portion HIV RT model while leaving the DNA where it fell into the proposed NS5B binding cleft. Looking closely at the the catalytic Mg2+ ions are modeled in green, these would be coordinated by the three aspartic acid carboxylates, (D220, D318 and D319). A (residues 440-455) in the thumb domain has been shifted to accommodate DNA, the hairpin is modeled into the minor groove, a possible binding site, particularly in the larger minor goove of dsRNA. There are noticeable steric clashes between the modeled DNA and the random coil at the end of the c-terminal domain where many of the deposited NS5B structures are disordered or have high b-factors so it is likely that the protein is mobile in this region and can thus accommodate RNA.

The template strand is seen entering through a gap in the fingers domain. An incoming dTTP that would extend the primer strand lines up with the NS5B active site and duplex DNA exits the enzyme through the large central hole in the closed active site formed by the unusual contacts between the fingers and thumb domains.

Figure 3.

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Figure 3 explores empirically determined sites of protein-ssRNA interactions. The highlighted were each identified without x-ray crystallography or NMR. These RNA binding peptides were identified by cross linking single stranded RNA to NS5B followed by a tryptic digest of the protein, then purification of the RNA bound peptide segments by affinity (for the RNA) chromatography. The segments of peptide that stuck to the column meaning they had been cross linked to RNA were then analyzed with MALDI mass spectrometry. It is interesting that all of the contacts were in the This could be in part due to the fact that single stranded RNA was cross linked to the enzyme, the fingers domain is thought to bind templating ssRNA while other regions of the polymerase would bind duplex RNA.





Figure 4 is a depiction of each of the protein products of NS5B genomic translation. The proteins coded for by the hepatitis C virus (HCV) genome all associate with the ER membrane. The proteins are translated as one large poly-protein that is enzymatically cleaved by both host and viral proteases. Of the several proteins that are coded for by HCV, three have been identified as relevant drug targets, these are the NS3 protease and helicase domains and the NS5B RNA dependent RNA polymerase. Currently the therapy for HCV is interferon therapy often in combination with ribavirin. This therapy however is inadequate as it is not effective in each genotype of HCV, it is not well tolerated, and expensive. For these reasons many academic and industrial laboratories have been working on developing novel inhibitors of NS5B. 

Image:PolyProtein.jpg

http://www.nature.com/nrmicro/journal/v5/n6/fig_tab/nrmicro1645_F4.html Figure 4.

Figure 5. NS5B in complex with ligands from deposited structures all superimposed on the 1.58Å resolution 2HAI. Ligands are from: 1C2P, 1CSJ, 1GX5, 1GX6, 1NB4, 1NB6, 1NB7, 1HNU, 1NHV, 1OS5, 1QUV, 1YUY, 1YV2, 1YVF, 1YVX, 1YVZ, 1Z4U, 2AWZ, 2AX0, 2AX1, 2BRK, 2BRL, 2D3U, 2D3Z, 2D41, 2GIQ, 2GIR, 2HWH, 2HWI, 2I1R, 2IJN, 2JC0, 2JC1, 3BR9, 3BSA, 3BSC, 3CIZ, 3CJ0, 3CJ2, 3CJ3, 3CJ4, 3CJ5.

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Figure 5 shows much of the x-ray crystallography work that has gone into NS5B to date. Each of the forty three structures included in the superposition contain at least one ligand, the ligands range from ions and small molecules to nucleotides and non-nucleoside analogue inhibitors. Positioning the structure in the familiar orientation with the colored as above, it is obvious that there are two primary areas where ligands are clustering. Several nucleotides, oligonucleotides and non-nucleoside analogue inhibitors can be found in the area right around the . There is another site that is about 30-35Å from the active site, an , where again ligands are clustering. There is a rGTP binding site here that seems to activate the enzyme and a nearby site where inhibitors bind and disrupt the activity of the enzyme.

The inhibitors that bind near the are thought to work by disrupting the primer grip site causing an inability of the enzyme to efficiently hold and extend a growing primer strand. The inhibitors that bind near the work through a poorly understood mechanism, several explanations for their ability to inhibit the enzyme have been proposed. The commonly proposed explanations are that these inhibitors lock the enzyme in an inactive conformation, inhibit binding of the rGTP that binds in the area and has been shown to stimulate activity, or that this interface is critical in protein-protein interactions and disruption of these interactions by the inhibitors disrupts an oligomerization of several NS5B protomers thus making each less efficient.

Reference

  • Li H, Tatlock J, Linton A, Gonzalez J, Borchardt A, Dragovich P, Jewell T, Prins T, Zhou R, Blazel J, Parge H, Love R, Hickey M, Doan C, Shi S, Duggal R, Lewis C, Fuhrman S. Identification and structure-based optimization of novel dihydropyrones as potent HCV RNA polymerase inhibitors. Bioorg Med Chem Lett. 2006 Sep 15;16(18):4834-8. Epub 2006 Jul 7. PMID:16824756 doi:10.1016/j.bmcl.2006.06.065
  • Ogata N, Alter HJ, Miller RH, Purcell RH. Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3392-6. PMID:1849654
  • Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature. 1998 Jan 15;391(6664):251-8. PMID:9440688 doi:http://dx.doi.org/10.1038/34593
  • O'Farrell D, Trowbridge R, Rowlands D, Jager J. Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation. J Mol Biol. 2003 Feb 28;326(4):1025-35. PMID:12589751
  • Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature. 1998 Jan 15;391(6664):251-8. PMID:9440688 doi:http://dx.doi.org/10.1038/34593
  • Kim YC, Russell WK, Ranjith-Kumar CT, Thomson M, Russell DH, Kao CC. Functional analysis of RNA binding by the hepatitis C virus RNA-dependent RNA polymerase. J Biol Chem. 2005 Nov 11;280(45):38011-9. Epub 2005 Sep 14. PMID:16166071 doi:10.1074/jbc.M508145200
  • Moradpour D, Penin F, Rice CM. Replication of hepatitis C virus. Nat Rev Microbiol. 2007 Jun;5(6):453-63. Epub 2007 May 8. PMID:17487147 doi:10.1038/nrmicro1645
  • Wang M, Ng KK, Cherney MM, Chan L, Yannopoulos CG, Bedard J, Morin N, Nguyen-Ba N, Alaoui-Ismaili MH, Bethell RC, James MN. Non-nucleoside analogue inhibitors bind to an allosteric site on HCV NS5B polymerase. Crystal structures and mechanism of inhibition. J Biol Chem. 2003 Mar 14;278(11):9489-95. Epub 2002 Dec 30. PMID:12509436 doi:10.1074/jbc.M209397200
  • Pfefferkorn JA, Greene ML, Nugent RA, Gross RJ, Mitchell MA, Finzel BC, Harris MS, Wells PA, Shelly JA, Anstadt RA, Kilkuskie RE, Kopta LA, Schwende FJ. Inhibitors of HCV NS5B polymerase. Part 1: Evaluation of the southern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid. Bioorg Med Chem Lett. 2005 May 16;15(10):2481-6. PMID:15863301 doi:10.1016/j.bmcl.2005.03.066

Superpositions in Figure 5 by Rould MA, and Villanueva NL

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