PDBsum entry 4obc

Viral protein, transferase

PDB id: 4obc

Contents

Protein chain

554 a.a.

Ligands

MES

GOL ×2

PG6

Metals

_CL

Waters ×206

PDB id:

4obc

Name:

Viral protein, transferase

Title:

Crystal structure of hcv polymerase ns5b genotype 2a jfh-1 isolate with the s15g, c223h, v321i resistance mutations against the guanosine analog gs-0938 (psi-3529238)

Structure:

RNA-directed RNA polymerase. Chain: a. Synonym: ns5b, p68. Engineered: yes. Mutation: yes

Source:

Hepatitis c virus jfh-1. Hcv. Organism_taxid: 356411. Strain: jfh-1. Gene: polg_hcvjf. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.50Å R-factor: 0.190 R-free: 0.223

Authors:

T.E.Edwards,J.Abendroth,T.C.Appleby

Key ref:

A.M.Lam et al. (2014). Molecular and structural basis for the roles of hepatitis C virus polymerase NS5B amino acids 15, 223, and 321 in viral replication and drug resistance. Antimicrob Agents Chemother, 58, 6861-6869. PubMed id: 25182647 DOI: 10.1128/AAC.03847-14

Date:

07-Jan-14 Release date: 10-Sep-14

Protein chain

Q99IB8  (POLG_HCVJF) -  Genome polyprotein from Hepatitis C virus genotype 2a (isolate JFH-1)

Seq: 3033 a.a.

Struc: 554 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: 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 4: E.C.3.4.22.- - ?????
• Enzyme class 5: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 6: 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

DOI no: 10.1128/AAC.03847-14

Antimicrob Agents Chemother 58:6861-6869 (2014)

PubMed id: 25182647

Molecular and structural basis for the roles of hepatitis C virus polymerase NS5B amino acids 15, 223, and 321 in viral replication and drug resistance.

A.M.Lam, T.E.Edwards, R.T.Mosley, E.Murakami, S.Bansal, C.Lugo, H.Bao, M.J.Otto, M.J.Sofia, P.A.Furman.

ABSTRACT

Resistance to the 2'-F-2'-C-methylguanosine monophosphate nucleotide hepatitis C virus (HCV) inhibitors PSI-352938 and PSI-353661 was associated with a combination of amino acid changes (changes of S to G at position 15 [S15G], C223H, and V321I) within the genotype 2a nonstructural protein 5B (NS5B), an RNA-dependent RNA polymerase. To understand the role of these residues in viral replication, we examined the effects of single and multiple point mutations on replication fitness and inhibition by a series of nucleotide analog inhibitors. An acidic residue at position 15 reduced replicon fitness, consistent with its proximity to the RNA template. A change of the residue at position 223 to an acidic or large residue reduced replicon fitness, consistent with its proposed proximity to the incoming nucleoside triphosphate (NTP). A change of the residue at position 321 to a charged residue was not tolerated, consistent with its position within a hydrophobic cavity. This triple resistance mutation was specific to both genotype 2a virus and 2'-F-2'-C-methylguanosine inhibitors. A crystal structure of the NS5B S15G/C223H/V321I mutant of the JFH-1 isolate exhibited rearrangement to a conformation potentially consistent with short primer-template RNA binding, which could suggest a mechanism of resistance accomplished through a change in the NS5B conformation, which was better tolerated by genotype 2a virus than by viruses of other genotypes.