6R1I

Structure of porcine Aichi virus polymerase

Summary for 6R1I

• Entry DOI: 10.2210/pdb6r1i/pdb
• Descriptor: Genome polyprotein (2 entities in total)
• Functional Keywords: virus, rna, polymerase, transferase
• Biological source: Porcine kobuvirus swine/S-1-HUN/2007/Hungary
• Total number of polymer chains: 2
• Total formula weight: 106677.47

Authors

Dubankova, A.,Boura, E. (deposition date: 2019-03-14, release date: 2019-10-09, Last modification date: 2024-01-24)

Primary citation

Dubankova, A.,Horova, V.,Klima, M.,Boura, E.
Structures of kobuviral and siciniviral polymerases reveal conserved mechanism of picornaviral polymerase activation.
J.Struct.Biol., 208:92-98, 2019

PubMed Abstract: RNA-dependent RNA polymerase 3D is a key enzyme for the replication of picornaviruses. The viral genome is translated into a single polyprotein that is subsequently proteolytically processed into matured products. The 3D enzyme arises from a stable 3CD precursor that has high proteolytic activity but no polymerase activity. Upon cleavage of the precursor the newly established N-terminus of 3D is liberated and inserts itself into a pocket on the surface of the 3D enzyme. The essential residue for this mechanism is the very first glycine that is conserved among almost all picornaviruses. However, kobuviruses and siciniviruses have a serine residue instead. Intrigued by this anomaly we sought to solve the crystal structure of these 3D enzymes. The structures revealed a unique fold of the 3D N-termini but the very first serine residues were inserted into a charged pocket in a similar manner as the glycine residue in other picornaviruses. These structures revealed a common underlying mechanism of 3D activation that lies in activation of the α10 helix containing a key catalytical residue Asp238 that forms a hydrogen bond with the 2' hydroxyl group of the incoming NTP nucleotide.

PubMed: 31415898
DOI: 10.1016/j.jsb.2019.08.004

Experimental method

X-RAY DIFFRACTION (2.634 Å)