PDBsum entry 2hcs

Transferase

PDB id: 2hcs

Contents

Protein chain

487 a.a. *

Metals

_ZN ×2

Waters ×106

* Residue conservation analysis

PDB id:

2hcs

Name:

Transferase

Title:

Crystal structure of RNA dependant RNA polymerase domain of west nile virus

Structure:

RNA-directed RNA polymerase (ns5). Chain: a. Fragment: RNA-directed RNA polymerase domain. Engineered: yes

Source:

Kunjin virus. Organism_taxid: 11077. Strain: kunjin. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.208 R-free: 0.243

Authors:

M.P.Egloff,H.Malet,Marseilles Structural Genomics Program @ Afmb (Msgp)

Key ref:

H.Malet et al. (2007). Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5. J Biol Chem, 282, 10678-10689. PubMed id: 17287213 DOI: 10.1074/jbc.M607273200

Date:

18-Jun-06 Release date: 06-Feb-07

Protein chain

P14335  (POLG_KUNJM) -  Genome polyprotein from Kunjin virus (strain MRM61C)

Seq: 3433 a.a.

Struc: 487 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.
• Reaction: a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
• Enzyme class 2: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺
• Enzyme class 3: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 4: E.C.3.4.21.91 - flavivirin.
• Reaction: Selective hydrolysis of Xaa-Xaa-|-Xbb bonds in which each of the Xaa can be either Arg or Lys and Xbb can be either Ser or Ala.
• 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: 10.1074/jbc.M607273200

J Biol Chem 282:10678-10689 (2007)

PubMed id: 17287213

Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5.

H.Malet, M.P.Egloff, B.Selisko, R.E.Butcher, P.J.Wright, M.Roberts, A.Gruez, G.Sulzenbacher, C.Vonrhein, G.Bricogne, J.M.Mackenzie, A.A.Khromykh, A.D.Davidson, B.Canard.

ABSTRACT

Viruses of the family Flaviviridae are important human and animal pathogens. Among them, the Flaviviruses dengue (DENV) and West Nile (WNV) cause regular outbreaks with fatal outcomes. The RNA-dependent RNA polymerase (RdRp) activity of the non-structural protein 5 (NS5) is a key activity for viral RNA replication. In this study, crystal structures of enzymatically active and inactive WNV RdRp domains were determined at 3.0- and 2.35-A resolution, respectively. The determined structures were shown to be mostly similar to the RdRps of the Flaviviridae members hepatitis C and bovine viral diarrhea virus, although with unique elements characteristic for the WNV RdRp. Using a reverse genetic system, residues involved in putative interactions between the RNA-cap methyltransferase (MTase) and the RdRp domain of Flavivirus NS5 were identified. This allowed us to propose a model for the structure of the full-length WNV NS5 by in silico docking of the WNV MTase domain (modeled from our previously determined structure of the DENV MTase domain) onto the RdRp domain. The Flavivirus RdRp domain structure determined here should facilitate both the design of anti-Flavivirus drugs and structure-function studies of the Flavivirus replication complex in which the multifunctional NS5 protein plays a central role.

Selected figure(s)

Figure 1.
FIGURE 1. Crystal structure of WNV POL1 and comparison with HCV RdRp. A, stereo view of a ribbon representation of WNV POL1 in its front orientation. The palm, thumb, and fingers domains and the priming loop are colored in green, red, dark blue, and purple, respectively. -Helices and -sheets are indicated. Insertions in WNV POL1 compared with HCV RdRp are displayed in yellow, and major structural differences are shown in orange. These and other figures were prepared with PyMOL. B, ribbon representation of HCV RdRp in its front orientation (50) (PDB code 1NB6). The color code is the same as in A. Insertions in HCV RdRp compared with WNV are colored in yellow.

Figure 3.
FIGURE 3. Divalent ion binding site in WNV POL. Stereo view of the calcium/magnesium ion non-catalytic binding site. The POL2 model is represented in green sticks and the corresponding electronic density in blue. The Ca^2+ ion is shown as a green sphere. The figure is centered on the aspartic acids of motifs A and C colored in yellow. Coordination with Asp^536 (motif A) and Asp^669 (motif C) are indicated by black dotted lines. Corresponding aspartic acids of motifs A and C in Phi6 (Asp^324, Asp^453, and Asp^454) (PDB code 1HI0) are represented in magenta sticks. The position of the two ions in the catalytic position, inferred from the Phi6 RdRp structure, is indicated in purple.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 10678-10689) copyright 2007.

Figures were selected by an automated process.