PDBsum entry 2e9t

Transferase/RNA

PDB id: 2e9t

Contents

Protein chains

474 a.a. *

DNA/RNA

Ligands

PPV ×2

Metals

_MG ×4

Waters ×65

* Residue conservation analysis

PDB id:

2e9t

Name:

Transferase/RNA

Title:

Foot-and-mouth disease virus RNA-polymerase RNA dependent in complex with a template-primer RNA and 5f-utp

Structure:

5'-r(p Up Ap Gp Gp Gp Cp Cp C)-3'. Chain: b, e. Engineered: yes. Other_details: RNA template. 5'-r( Gp Gp Gp Cp Cp Cp (5Fu))-3'. Chain: c, f. Engineered: yes. Other_details: RNA primer. RNA-dependent RNA polymerase.

Source:

Synthetic: yes. Foot-and-mouth disease virus c-s8c1. Organism_taxid: 244367. Strain: c-s8c1. Gene: 3d. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.60Å R-factor: 0.236 R-free: 0.289

Authors:

C.Ferrer-Orta,A.Arias,R.Perez-Luque,C.Escarmis,E.Domingo,N.Verdaguer

Key ref:

C.Ferrer-Orta et al. (2007). Sequential structures provide insights into the fidelity of RNA replication. Proc Natl Acad Sci U S A, 104, 9463-9468. PubMed id: 17517631 DOI: 10.1073/pnas.0700518104

Date:

26-Jan-07 Release date: 26-Jun-07

Protein chains

Q9QCE4  (Q9QCE4_9PICO) -  Genome polyprotein from Foot and mouth disease virus C

Seq: 2327 a.a.

Struc: 474 a.a.

DNA/RNA chains

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

G-G-G-C-C-C-5FU 7 bases

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

G-G-G-C-C-C-5FU 7 bases

Enzyme reactions

• Enzyme class 1: E.C.3.4.22.46 - L-peptidase.
• Reaction: Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-.
• 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 + H2O = ribonucleoside 5'-diphosphate + phosphate + H(+) (Bound ligand (Het Group name = PPV) matches with 55.56% similarity)

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: 10.1073/pnas.0700518104

Proc Natl Acad Sci U S A 104:9463-9468 (2007)

PubMed id: 17517631

Sequential structures provide insights into the fidelity of RNA replication.

C.Ferrer-Orta, A.Arias, R.Pérez-Luque, C.Escarmís, E.Domingo, N.Verdaguer.

ABSTRACT

RNA virus replication is an error-prone event caused by the low fidelity of viral RNA-dependent RNA polymerases. Replication fidelity can be decreased further by the use of mutagenic ribonucleoside analogs to a point where viral genetic information can no longer be maintained. For foot-and-mouth disease virus, the antiviral analogs ribavirin and 5-fluorouracil have been shown to be mutagenic, contributing to virus extinction through lethal mutagenesis. Here, we report the x-ray structure of four elongation complexes of foot-and-mouth disease virus polymerase 3D obtained in presence of natural substrates, ATP and UTP, or mutagenic nucleotides, ribavirin triphosphate and 5-fluorouridine triphosphate with different RNAs as template-primer molecules. The ability of these complexes to synthesize RNA in crystals allowed us to capture different successive replication events and to define the critical amino acids involved in (i) the recognition and positioning of the incoming nucleotide or analog; (ii) the positioning of the acceptor base of the template strand; and (iii) the positioning of the 3'-OH group of the primer nucleotide during RNA replication. The structures identify key interactions involved in viral RNA replication and provide insights into the molecular basis of the low fidelity of viral RNA polymerases.

Selected figure(s)

Figure 1.
Fig. 1. Structure of FMDV 3D catalytic complexes. Molecular surface of the polymerase (gray) is shown, with the position of the rNTP substrates and the trajectory of RNA template–primer and duplex product in two different complexes: the 3D·GCAUGGGCCC·ATP/UTP (A) and the 3D·GCAUGGGCCC-RTP (B). The N-terminal residues (residues 34–48) and residues at the top of the NTP tunnel (163–180) of 3D are omitted to show the substrate cavities. RNA molecules are shown in yellow (template strands) and green (primer strands). (A) The UTP substrate is shown in cyan. (B) The position of the antiviral mutagen RTP is shown in orange. Metal ions are shown as red spheres.

Figure 2.
Fig. 2. Conserved interactions between the FMDV 3D and the different RNA template–primers. The polymerase regions involved in contacts with the RNA molecule are explicitly labeled. The template and primer strands of the RNA molecule are shown in yellow and green, respectively; atoms are displayed in atom-type code, and hydrogen bonds are dashed lines in black. The template strand contacts mainly with residues in the fingers subdomain (blue). The 5' overhang region of the template binds the template channel, where the different residues of the N-terminal region and the loop 4– 3 of the polymerase drive the ssRNA to the active-site cavity (Lower Left). The template strand of the dsRNA product contacts different residues of helix 7 and the loop 9– 11 in its exit through the central cavity of the enzyme (Upper Left). The primer strand interacts with motifs C and E of the palm subdomain, shown in magenta (Upper Right) and with helix 14 of the thumb, shown in red (Lower Right).

Figures were selected by an automated process.