PDBsum entry 3bsn

Transferase/RNA

PDB id: 3bsn

Contents

Protein chain

479 a.a. *

DNA/RNA

Ligands

GOL ×4

N5C

Metals

_MN ×3

Waters ×347

* Residue conservation analysis

PDB id:

3bsn

Name:

Transferase/RNA

Title:

Norwalk virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA

Structure:

RNA dependent RNA polymerase. Chain: a. Engineered: yes. RNA (5'-r( Up Gp Cp Cp Cp Gp Gp G)-3'). Chain: p. Engineered: yes. RNA (5'-r( Up Gp Cp Cp Cp Gp Gp Gp (N5m))-3'). Chain: t. Engineered: yes

Source:

Norwalk virus. Organism_taxid: 11983. Strain: ast6139/01/sp. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: chemically synthesized self-complementary RNA oligonucleotide with 2-base overhang. Oligonucleotide that was extended by a single 5-nitrocytidine

Resolution:

1.80Å R-factor: 0.203 R-free: 0.236

Authors:

D.F.Zamyatkin,K.K.S.Ng

Key ref:

D.F.Zamyatkin et al. (2008). Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase. J Biol Chem, 283, 7705-7712. PubMed id: 18184655 DOI: 10.1074/jbc.M709563200

Date:

26-Dec-07 Release date: 08-Jan-08

Protein chain

Q70ET3  (Q70ET3_9CALI) -  Genome polyprotein (Fragment) from Norwalk virus

Seq: 838 a.a.

Struc: 479 a.a.

DNA/RNA chains

U-G-C-C-C-G-G-G 8 bases

U-G-C-C-C-G-G-G-N5M 9 bases

Enzyme reactions

• Enzyme class 1: E.C.3.4.22.66 - calicivirin.
• Enzyme class 2: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

ribonucleoside 5'-triphosphate (Bound ligand (Het Group name = N5C) matches with 63.64% similarity) + H2O = ribonucleoside 5'-diphosphate + 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

Key reference

DOI no: 10.1074/jbc.M709563200

J Biol Chem 283:7705-7712 (2008)

PubMed id: 18184655

Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase.

D.F.Zamyatkin, F.Parra, J.M.Alonso, D.A.Harki, B.R.Peterson, P.Grochulski, K.K.Ng.

ABSTRACT

Crystal structures of Norwalk virus polymerase bound to an RNA primer-template duplex and either the natural substrate CTP or the inhibitor 5-nitrocytidine triphosphate have been determined to 1.8A resolution. These structures reveal a closed conformation of the polymerase that differs significantly from previously determined open structures of calicivirus and picornavirus polymerases. These closed complexes are trapped immediately prior to the nucleotidyl transfer reaction, with the triphosphate group of the nucleotide bound to two manganese ions at the active site, poised for reaction to the 3'-hydroxyl group of the RNA primer. The positioning of the 5-nitrocytidine triphosphate nitro group between the alpha-phosphate and the 3'-hydroxyl group of the primer suggests a novel, general approach for the design of antiviral compounds mimicking natural nucleosides and nucleotides.

Selected figure(s)

Figure 2.
FIGURE 2. Stereoscopic overall views of (A, top; C, side) NV RdRP·RNA·Mn^2+·NCT complex and (B, top; D, side) uncomplexed NV RdRP (Protein Data Bank code 1SH0 (11)). The primer (yellow) and template (magenta) strands of RNA, NCT (red), and Mn^2+ (pink) are drawn. The C-terminal tail of unbound NV RdRP is highlighted in red. The largest conformational changes in the thumb and fingers domains following the binding of RNA are highlighted with arrows.

Figure 3.
FIGURE 3. Stereoscopic views of the active site of the NCT (A and C) and CTP (B and D) complexes. In panels A and B, coordination bonds (red dashes) with Mn^2+ ions A and B (pink spheres), and hydrogen bonds (red dashes) between the bound nucleotide (magenta), key water molecules (red spheres), and the protein are drawn. In panels C and D, Arg-182, the bound nucleotide, Mn^2+ ions, and the terminal nucleotide of the primer were removed prior to 20 rounds of refinement and (|F[o]| - |F[c]|) electron density map calculation (3 contour). Figs. 2 and 3 were prepared using PyMOL (38).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 7705-7712) copyright 2008.

Figures were selected by the author.