PDBsum entry 8ohm

Helicase

PDB id: 8ohm

Contents

Protein chain

435 a.a. *

Waters ×140

* Residue conservation analysis

PDB id:

8ohm

Name:

Helicase

Title:

Crystal structure of RNA helicase from genotype 1b hepatitis c virus: mechanism of unwinding duplex RNA

Structure:

RNA helicase. Chain: a. Engineered: yes

Source:

Hepatitis c virus. Organism_taxid: 11103. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.233 R-free: 0.303

Authors:

H.S.Cho,N.C.Ha,L.W.Kang,B.H.Oh

Key ref:

H.S.Cho et al. (1998). Crystal structure of RNA helicase from genotype 1b hepatitis C virus. A feasible mechanism of unwinding duplex RNA. J Biol Chem, 273, 15045-15052. PubMed id: 9614113 DOI: 10.1074/jbc.273.24.15045

Date:

13-Mar-98 Release date: 20-Apr-99

Protein chain

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

Seq: 3010 a.a.

Struc: 435 a.a.*

* PDB and UniProt seqs differ at 16 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

DOI no: 10.1074/jbc.273.24.15045

J Biol Chem 273:15045-15052 (1998)

PubMed id: 9614113

Crystal structure of RNA helicase from genotype 1b hepatitis C virus. A feasible mechanism of unwinding duplex RNA.

H.S.Cho, N.C.Ha, L.W.Kang, K.M.Chung, S.H.Back, S.K.Jang, B.H.Oh.

ABSTRACT

Crystal structure of RNA helicase domain from genotype 1b hepatitis C virus has been determined at 2.3 A resolution by the multiple isomorphous replacement method. The structure consists of three domains that form a Y-shaped molecule. One is a NTPase domain containing two highly conserved NTP binding motifs. Another is an RNA binding domain containing a conserved RNA binding motif. The third is a helical domain that contains no beta-strand. The RNA binding domain of the molecule is distinctively separated from the other two domains forming an interdomain cleft into which single stranded RNA can be modeled. A channel is found between a pair of symmetry-related molecules which exhibit the most extensive crystal packing interactions. A stretch of single stranded RNA can be modeled with electrostatic complementarity into the interdomain cleft and continuously through the channel. These observations suggest that some form of this dimer is likely to be the functional form that unwinds double stranded RNA processively by passing one strand of RNA through the channel and passing the other strand outside of the dimer. A "descending molecular see-saw" model is proposed that is consistent with directionality of unwinding and other physicochemical properties of RNA helicases.

Selected figure(s)

Figure 3.
Fig. 3. Interaction of the D^290ECH and the T322AT sequence of HCV RNA helicase. Note Asp290, Glu291, and His293 that form a part of the active site cavity are on a loop structure and point in the same direction. The backbones of the DECH motif and TAT sequence are in cyan and magenta, respectively, and the side chains are in green. The white dotted line indicates the hydrogen bond between His293 and Thr322.

Figure 7.
Fig. 7. A side view of "descending molecular see-saw" model for the translocation of HCV RNA helicase along ssRNA. The dimer (left) translocates along the ssRNA (right) by a rotation of about 60° (with respect to the axis of the RNA double helix) along an axis passing the front part of RNA binding motif. The right figure represents a translocation of the dimer by a half-turn of RNA with respect to the location of the dimer on ssRNA in the left figure. For clear presentation of the translational motion, the two figures are shown with orientations different by 180° with respect to each step. Figs. 1, 3, and 5 were produced using the program MOLSCRIPT, Fig. 2 using the program O, Fig. 4 using the program GRASP, and Figs. 6 and 7 using the program QUANTA.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 15045-15052) copyright 1998.

Figures were selected by an automated process.