PDBsum entry 1gx6

Transferase

PDB id: 1gx6

Contents

Protein chain

531 a.a. *

Ligands

UTP ×3

Metals

_MN ×5

Waters ×485

* Residue conservation analysis

PDB id:

1gx6

Name:

Transferase

Title:

Hepatitis c virus RNA polymerase in complex with utp and manganese

Structure:

RNA-directed RNA polymerase. Chain: a. Fragment: catalytic domain, residues 2420-2950. Engineered: yes

Source:

Hepatitis c virus (isolate bk). Hcv. Organism_taxid: 11105. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.85Å R-factor: 0.197 R-free: 0.229

Authors:

S.Bressanelli,F.A.Rey

Key ref:

S.Bressanelli et al. (2002). Structural analysis of the hepatitis C virus RNA polymerase in complex with ribonucleotides. J Virol, 76, 3482-3492. PubMed id: 11884572

Date:

27-Mar-02 Release date: 10-Apr-02

Protein chain

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

Seq: 3010 a.a.

Struc: 531 a.a.

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

RNA(n) + ribonucleoside 5'-triphosphate = RNA(n+1) (Bound ligand (Het Group name = UTP) matches with 69.23% similarity) + 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⁺

ATP (Bound ligand (Het Group name = UTP) matches with 81.82% similarity) + 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 76:3482-3492 (2002)

PubMed id: 11884572

Structural analysis of the hepatitis C virus RNA polymerase in complex with ribonucleotides.

S.Bressanelli, L.Tomei, F.A.Rey, R.De Francesco.

ABSTRACT

We report here the results of a systematic high-resolution X-ray crystallographic analysis of complexes of the hepatitis C virus (HCV) RNA polymerase with ribonucleoside triphosphates (rNTPs) and divalent metal ions. An unexpected observation revealed by this study is the existence of a specific rGTP binding site in a shallow pocket at the molecular surface of the enzyme, 30 A away from the catalytic site. This previously unidentified rGTP pocket, which lies at the interface between fingers and thumb, may be an allosteric regulatory site and could play a role in allowing alternative interactions between the two domains during a possible conformational change of the enzyme required for efficient initiation. The electron density map at 1.7-A resolution clearly shows the mode of binding of the guanosine moiety to the enzyme. In the catalytic site, density corresponding to the triphosphates of nucleotides bound to the catalytic metals was apparent in each complex with nucleotides. Moreover, a network of triphosphate densities was detected; these densities superpose to the corresponding moieties of the nucleotides observed in the initiation complex reported for the polymerase of bacteriophage phi6, strengthening the proposal that the two enzymes initiate replication de novo by similar mechanisms. No equivalent of the protein stacking platform observed for the priming nucleotide in the phi6 enzyme is present in HCV polymerase, however, again suggesting that a change in conformation of the thumb domain takes place upon template binding to allow for efficient de novo initiation of RNA synthesis.