PDBsum entry 1os5

Transferase

PDB id: 1os5

Contents

Protein chain

563 a.a. *

Ligands

NH1

Waters ×560

* Residue conservation analysis

PDB id:

1os5

Name:

Transferase

Title:

Crystal structure of hcv ns5b RNA polymerase complexed with a novel non-competitive inhibitor.

Structure:

Hepatitis c virus ns5b RNA polymerase. Chain: a. Engineered: yes. Mutation: yes

Source:

Hepatitis c virus. Organism_taxid: 31647. Strain: subtype 1b. Gene: ns5b. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.207 R-free: 0.251

Authors:

R.A.Love,H.E.Parge,X.Yu,M.J.Hickey,W.Diehl,J.Gao,H.Wriggers,A.Ekker, L.Wang,J.A.Thomson,P.S.Dragovich,S.A.Fuhrman

Key ref:

R.A.Love et al. (2003). Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C virus NS5B RNA polymerase enzyme. J Virol, 77, 7575-7581. PubMed id: 12805457

Date:

18-Mar-03 Release date: 18-Mar-04

Protein chain

P26663  (POLG_HCVBK) -  Genome polyprotein from Hepatitis C virus genotype 1b (isolate BK)

Seq: 3010 a.a.

Struc: 563 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: E.C.3.4.21.98 - hepacivirin.
• Reaction: Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
• Enzyme class 3: E.C.3.4.22.- - ?????
• Enzyme class 4: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 5: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

J Virol 77:7575-7581 (2003)

PubMed id: 12805457

Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C virus NS5B RNA polymerase enzyme.

R.A.Love, H.E.Parge, X.Yu, M.J.Hickey, W.Diehl, J.Gao, H.Wriggers, A.Ekker, L.Wang, J.A.Thomson, P.S.Dragovich, S.A.Fuhrman.

ABSTRACT

The virus-encoded nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) is an RNA-dependent RNA polymerase and is absolutely required for replication of the virus. NS5B exhibits significant differences from cellular polymerases and therefore has become an attractive target for anti-HCV therapy. Using a high-throughput screen, we discovered a novel NS5B inhibitor that binds to the enzyme noncompetitively with respect to nucleotide substrates. Here we report the crystal structure of NS5B complexed with this small molecule inhibitor. Unexpectedly, the inhibitor is bound within a narrow cleft on the protein's surface in the "thumb" domain, about 30 A from the enzyme's catalytic center. The interaction between this inhibitor and NS5B occurs without dramatic changes to the structure of the protein, and sequence analysis suggests that the binding site is conserved across known HCV genotypes. Possible mechanisms of inhibition include perturbation of protein dynamics, interference with RNA binding, and disruption of enzyme oligomerization.