PDBsum entry 1quv

Transferase

PDB id: 1quv

Contents

Protein chain

553 a.a. *

Waters ×284

* Residue conservation analysis

PDB id:

1quv

Name:

Transferase

Title:

Crystal structure of the RNA directed RNA polymerase of hepatitis c virus

Structure:

Protein (RNA-directed RNA polymerase). Chain: a. Fragment: residues 2420-2989. Synonym: ns5b. Engineered: yes. Mutation: yes

Source:

Hepatitis c virus. Organism_taxid: 11103. Strain: 1b (bk). Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.50Å R-factor: 0.223 R-free: 0.316

Authors:

H.Ago,M.Miyano,T.Adachi,N.Habuka

Key ref:

H.Ago et al. (1999). Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Structure, 7, 1417-1426. PubMed id: 10574802 DOI: 10.1016/S0969-2126(00)80031-3

Date:

04-Jul-99 Release date: 05-Nov-99

Protein chain

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

Seq: 3010 a.a.

Struc: 553 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
• 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

DOI no: 10.1016/S0969-2126(00)80031-3

Structure 7:1417-1426 (1999)

PubMed id: 10574802

Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus.

H.Ago, T.Adachi, A.Yoshida, M.Yamamoto, N.Habuka, K.Yatsunami, M.Miyano.

ABSTRACT

BACKGROUND: Hepatitis C virus (HCV) is the major etiological agent of hepatocellular carcinoma, and HCV RNA-dependent RNA polymerase (RdRp) is one of the main potential targets for anti-HCV agents. HCV RdRp performs run-off copying replication in an RNA-selective manner for the template-primer duplex and the substrate, but the structural basis of this reaction mechanism has still to be elucidated. RESULTS: The three-dimensional structure of HCV RdRp was determined by X-ray crystallography at 2.5 A resolution. The compact HCV RdRp structure resembles a right hand, but has more complicated fingers and thumb domains than those of the other known polymerases, with a novel alpha-helix-rich subdomain (alpha fingers) as an addition to the fingers domain. The other fingers subdomain (beta fingers) is folded in the same manner as the fingers domain of human immunodeficiency virus (HIV) reverse transcriptase (RT), another RNA-dependent polymerase. The ribose-recognition site of HCV RdRp is constructed of hydrophilic residues, unlike those of DNA polymerases. The C-terminal region of HCV RdRp occupies the putative RNA-duplex-binding cleft. CONCLUSIONS: The structural basis of the RNA selectivity of HCV RdRp was elucidated from its crystal structure. The putative substrate-binding site with a shallow hydrophilic cavity should have ribonucleoside triphosphate (rNTP) as the preferred substrate. We propose that the unique alpha fingers might represent a common structural discriminator of the template-primer duplex that distinguishes between RNA and DNA during the replication of positive single-stranded RNA by viral RdRps. The C-terminal region might exert a regulatory function on the initiation and activity of HCV RdRp.

Selected figure(s)

Figure 3.
Figure 3. Structure comparison of HCV RdRp with poliovirus RdRp and HIV RT and with the Mrf-2 DNA-binding domain. (a) Stereoview of superimposed wire models of the a- and b-fingers subdomains and palm domain of HCV RdRp and the corresponding portions of poliovirus RdRp [13] and the ternary complex of HIV RT [24]. The a fingers, b fingers, and palm of HCV RdRp are shown in green, cyan, and pink, respectively. Poliovirus RdRp is shown in silver and HIV RT is shown in gold. The positively charged residues mentioned in the text are represented by blue balls and sticks. In the b-fingers subdomain, the basic residues are Lys51, Arg48, Arg158, Lys155 and Lys141 from the outside. In the a fingers, the residues are Lys98, Arg168, Lys172, Lys90, Arg109 and Lys106 from the top right in a clockwise direction. (b) Stereoview of superimposed wire models of the thumb domains of HCV RdRp (violet), poliovirus RdRp (silver) [13] and HIV RT (gold) [24]. (c) Stereoview of superimposed wire models of the a-fingers region, including its connecting b1-b2 loop in the b-fingers subdomain (residues 74-189), of HCV RdRp (blue) and the Mrf-2 DNA-binding domain (red) [25].

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1417-1426) copyright 1999.

Figure was selected by an automated process.