2PGG

Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1

Summary for 2PGG

• Entry DOI: 10.2210/pdb2pgg/pdb
• Descriptor: RNA-directed RNA polymerase (2 entities in total)
• Functional Keywords: polymerase, rdrp, birnavirus, ibdv, permutation, dsrna virus, transferase
• Biological source: Infectious bursal disease virus (Gumboro virus)
• Cellular location: Virion (By similarity): Q9Q6Q5
• Total number of polymer chains: 1
• Total formula weight: 86504.80

Authors

Pan, J.,Vakharia, V.N.,Tao, Y.J. (deposition date: 2007-04-09, release date: 2007-05-22, Last modification date: 2024-02-21)

Primary citation

Pan, J.,Vakharia, V.N.,Tao, Y.J.
The structure of a birnavirus polymerase reveals a distinct active site topology.
Proc.Natl.Acad.Sci.Usa, 104:7385-7390, 2007

PubMed Abstract: Single-subunit polymerases are universally encoded in both cellular organisms and viruses. Their three-dimensional structures have the shape of a right-hand with the active site located in the palm region, which has a topology similar to that of the RNA recognition motif (RRM) found in many RNA-binding proteins. Considering that polymerases have well conserved structures, it was surprising that the RNA-dependent RNA polymerases from birnaviruses, a group of dsRNA viruses, have their catalytic motifs arranged in a permuted order in sequence. Here we report the 2.5 A structure of a birnavirus VP1 in which the polymerase palm subdomain adopts a new active site topology that has not been previously observed in other polymerases. In addition, the polymerase motif C of VP1 has the sequence of -ADN-, a highly unusual feature for RNA-dependent polymerases. Through site-directed mutagenesis, we have shown that changing the VP1 motif C from -ADN- to -GDD- results in a mutant with an increased RNA synthesis activity. Our results indicate that the active site topology of VP1 may represent a newly developed branch in polymerase evolution, and that birnaviruses may have acquired the -ADN- mutation to control their growth rate.

PubMed: 17456597
DOI: 10.1073/pnas.0611599104

Experimental method

X-RAY DIFFRACTION (2.5 Å)