3CDW

Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3Dpol) in complex with protein primer VPg and a pyrophosphate

Summary for 3CDW

• Entry DOI: 10.2210/pdb3cdw/pdb
• Related: 1XR5 2E9Z 2F8E 2ILZ 3CDU
• Descriptor: RNA-directed RNA polymerase 3D-POL, Protein 3B, CHLORIDE ION, ... (7 entities in total)
• Functional Keywords: coxsackievirus, rna-dependent rna polymerase, protein primer, vpg, vizier viral enzymes involved in replication, transferase-viral protein complex, transferase/viral protein
• Biological source: Coxsackievirus B3; More
• Cellular location: Protein VP2: Virion. Protein VP3: Virion. Protein VP1: Virion. Protein 2B: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 2C: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3A: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3B: Virion (Potential). Picornain 3C: Host cytoplasm (Potential). RNA-directed RNA polymerase 3D-POL: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential): P03313 P03313
• Total number of polymer chains: 2
• Total formula weight: 58955.59

Authors

Gruez, A.,Selisko, B.,Roberts, M.,Bricogne, G.,Bussetta, C.,Canard, B. (deposition date: 2008-02-27, release date: 2008-07-22, Last modification date: 2023-11-01)

Primary citation

Gruez, A.,Selisko, B.,Roberts, M.,Bricogne, G.,Bussetta, C.,Jabafi, I.,Coutard, B.,De Palma, A.M.,Neyts, J.,Canard, B.
The crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase in complex with its protein primer VPg confirms the existence of a second VPg binding site on Picornaviridae polymerases
J.Virol., 82:9577-9590, 2008

PubMed Abstract: The RNA-dependent RNA polymerase (RdRp) is a central piece in the replication machinery of RNA viruses. In picornaviruses this essential RdRp activity also uridylates the VPg peptide, which then serves as a primer for RNA synthesis. Previous genetic, binding, and biochemical data have identified a VPg binding site on poliovirus RdRp and have shown that is was implicated in VPg uridylation. More recent structural studies have identified a topologically distinct site on the closely related foot-and-mouth disease virus RdRp supposed to be the actual VPg-primer-binding site. Here, we report the crystal structure at 2.5-A resolution of active coxsackievirus B3 RdRp (also named 3D(pol)) in a complex with VPg and a pyrophosphate. The pyrophosphate is situated in the active-site cavity, occupying a putative binding site either for the coproduct of the reaction or an incoming NTP. VPg is bound at the base of the thumb subdomain, providing first structural evidence for the VPg binding site previously identified by genetic and biochemical methods. The binding mode of VPg to CVB3 3D(pol) at this site excludes its uridylation by the carrier 3D(pol). We suggest that VPg at this position is either uridylated by another 3D(pol) molecule or that it plays a stabilizing role within the uridylation complex. The CVB3 3D(pol)/VPg complex structure is expected to contribute to the understanding of the multicomponent VPg-uridylation complex essential for the initiation of genome replication of picornaviruses.

PubMed: 18632861
DOI: 10.1128/JVI.00631-08

Experimental method

X-RAY DIFFRACTION (2.5 Å)