PDBsum entry 2f8e

Transferase

PDB id: 2f8e

Contents

Protein chains

474 a.a. *

15 a.a. *

Ligands

U5P

Metals

_MG

_MN

* Residue conservation analysis

PDB id:

2f8e

Name:

Transferase

Title:

Foot and mouth disease virus RNA-dependent RNA polymerase in complex with uridylylated vpg protein

Structure:

RNA-dependent RNA polymerase. Chain: x. Engineered: yes. Vpg protein. Chain: a. Engineered: yes

Source:

Foot-and-mouth disease virus - typE C. Organism_taxid: 12116. Strain: c-s8c1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: vpg was prepared by solid phase peptide synthesis

Biol. unit:

Dimer (from PQS)

Resolution:

2.90Å R-factor: 0.237 R-free: 0.284

Authors:

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

Key ref:

C.Ferrer-Orta et al. (2006). The structure of a protein primer-polymerase complex in the initiation of genome replication. EMBO J, 25, 880-888. PubMed id: 16456546 DOI: 10.1038/sj.emboj.7600971

Date:

02-Dec-05 Release date: 28-Mar-06

Protein chain

Q0QEE0  (Q0QEE0_9PICO) -  Genome polyprotein from Foot and mouth disease virus C

Seq: 1994 a.a.

Struc: 474 a.a.

Protein chain

Q9DS05  (Q9DS05_FMDA1) -  Polyprotein (Fragment) from Foot-and-mouth disease virus serotype Asia-1

Seq: 71 a.a.

Struc: 15 a.a.*

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

Enzyme reactions

• Enzyme class: Chain X: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/sj.emboj.7600971

EMBO J 25:880-888 (2006)

PubMed id: 16456546

The structure of a protein primer-polymerase complex in the initiation of genome replication.

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

ABSTRACT

Picornavirus RNA replication is initiated by the covalent attachment of a UMP molecule to the hydroxyl group of a tyrosine in the terminal protein VPg. This reaction is carried out by the viral RNA-dependent RNA polymerase (3D). Here, we report the X-ray structure of two complexes between foot-and-mouth disease virus 3D, VPg1, the substrate UTP and divalent cations, in the absence and in the presence of an oligoadenylate of 10 residues. In both complexes, VPg fits the RNA binding cleft of the polymerase and projects the key residue Tyr3 into the active site of 3D. This is achieved by multiple interactions with residues of motif F and helix alpha8 of the fingers domain and helix alpha13 of the thumb domain of the polymerase. The complex obtained in the presence of the oligoadenylate showed the product of the VPg uridylylation (VPg-UMP). Two metal ions and the catalytic aspartic acids of the polymerase active site, together with the basic residues of motif F, have been identified as participating in the priming reaction.

Selected figure(s)

Figure 1.
Figure 1 Structure of the primer protein VPg in a complex with 3D. (A) Stereo view of a sigma A weighted |F[o]|-|F[c]| electron density map at 2.9 Å resolution and contoured at 3.0 around the VPg-UMP molecule (The VPg-UMP and ions were omitted from the phasing model). The 15 amino acids of VPg, the UMP covalently linked to the protein and the metal ions are placed inside the density in ball and stick representation colored in atom type code. Names for all residues are explicitly labeled in one letter code. (B) Details of the interactions seen in the active site of the 3D polymerase during the uridylylation reaction. The residues Pro2, Tyr3 and Ala4 of VPg are shown in sticks in red and the UMP, covalently linked to the hydroxyl group of Tyr3, in light green. The divalent cations Mn2+ and Mg2+ are shown as magenta and orange spheres, respectively, and the anomalous difference Fourier map is shown as a chicken wire in blue. The 3D amino acids involved in direct hydrogen bonds with ions and the uridylylated tyrosine are shown in ball and sticks in atom type code, and the hydrogen bonds appear as dashed lines. All residues are explicitly labeled. The predicted position of the oligo(A) template strand (dark green) was determined using the 3D-RNA template-primer complex (PDB entry 1WNE) as a guide.

Figure 3.
Figure 3 VPg-3D polymerase interactions. (A) Structure of the VPg primer protein (red) with the contacting residues of the 3D polymerase shown in different colors. Four different regions of the polymerase molecule contact VPg residues E166, I167, R168, K172 and R179, belonging to motif F of fingers (orange), together with residues T407, A410 and I411 of the thumb domain (light blue), interact with the N-terminal moiety of VPg, stabilizing the conformation of Y3 in the active site cavity. In addition, residues E166, I167 of motif F (orange), K387 and R388 of motif E (dark blue) and T407, A410 and I411 of helix 13 (light blue) interact with the central part of the VPg protein. Finally, the 3D residues G216, C217 and P219, located at the beginning of helix 8 (light blue) in the fingers domain, together with the side chain of Y336 within the C motif (yellow) of the palm domain, establish hydrophobic contacts with R11 at the exit of the polymerase cavity. (B) Structure of the uridylylated VPg protein (shown in red and the linked UMP in green) with the contacting residues of the 3D polymerase shown in blue. In addition to the interactions described in (A), amino acids D245 of motif A (pink) and D338 of motif C (yellow) are placed in the correct orientation for the catalysis of the phosphodiester linkage in the active site of the 3D protein.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 880-888) copyright 2006.

Figures were selected by an automated process.