PDBsum entry 3kms

Transferase/RNA

PDB id: 3kms

Contents

Protein chain

476 a.a. *

DNA/RNA

Metals

_MG

Waters ×68

* Residue conservation analysis

PDB id:

3kms

Name:

Transferase/RNA

Title:

G62s mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA trigonal structure

Structure:

3d polymerase. Chain: a. Synonym: RNA dependent RNA polymerase. Engineered: yes. Mutation: yes. RNA (5'-r( Ap Up Gp Gp Gp Cp C)-3'). Chain: b. Engineered: yes. RNA (5'-r( Gp Gp Cp Cp C)-3').

Source:

Foot-and-mouth disease virus - typE C. Organism_taxid: 12116. Strain: c-s8c1. Gene: 3d. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes. Synthetic: yes

Resolution:

2.20Å R-factor: 0.238 R-free: 0.266

Authors:

C.Ferrer-Orta,N.Verdaguer,R.Perez-Luque

Key ref:

C.Ferrer-Orta et al. (2010). Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin. J Virol, 84, 6188-6199. PubMed id: 20392853

Date:

11-Nov-09 Release date: 07-Jul-10

Protein chain

Q9QCE3  (Q9QCE3_9PICO) -  Genome polyprotein from Foot and mouth disease virus C

Seq: 2327 a.a.

Struc: 476 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

A-U-G-G-G-C-C 7 bases

G-G-C-C-C 5 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⁺

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

J Virol 84:6188-6199 (2010)

PubMed id: 20392853

Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin.

C.Ferrer-Orta, M.Sierra, R.Agudo, I.de la Higuera, A.Arias, R.Pérez-Luque, C.Escarmís, E.Domingo, N.Verdaguer.

ABSTRACT

Passage of poliovirus (PV) or foot-and-mouth disease virus (FMDV) in the presence of ribavirin selected for viruses with decreased sensitivity to R, which included different mutations in their polymerase (3D): G64S located in the finger subdomain in the case of PV and M296I located within loop beta9-alpha11 at the active site in the case of FMDV. To investigate why disparate substitutions were selected in two closely related 3Ds, we constructed FMDVs with a 3D that included either G62S (the equivalent replacement in FMDV of PV G64S), M296I, or both substitutions. G62S, but not M296I, inflicts upon FMDV a strong selective disadvantage which is partially compensated for by the substitution M296I. The corresponding mutant polymerases, 3D(G62S), 3D(M296I), and 3D(G62S-M296I), were analyzed functionally and structurally. G62S in 3D impairs RNA-binding, polymerization, and R monophosphate incorporation activities. The X-ray structures of the 3D(G62S)-RNA, 3D(M296I)-RNA, and 3D(G62S-M296I)-RNA complexes show that although the two positions are separated by 13.1 A, the loops where the replacements reside are tightly connected through an extensive network of interactions that reach the polymerase active site. In particular, G62S seems to restrict the flexibility of loop beta9-alpha11 and, as a consequence, the flexibility of the active site and its ability to bind the RNA template. Thus, a localized change in the finger subdomain of 3D may affect the catalytic domain. The results provide a structural interpretation of why different amino acid substitutions were selected to confer R resistance in closely related viruses and reveal a complex network of intra-3D interactions that can affect the recognition of both the RNA template and incoming nucleotide.