1S48

Crystal structure of RNA-dependent RNA polymerase construct 1 (residues 71-679) from BVDV

Summary for 1S48

• Entry DOI: 10.2210/pdb1s48/pdb
• Related: 1S49 1S4F
• Descriptor: RNA-dependent RNA polymerase (1 entity in total)
• Functional Keywords: polymerase, primer independent initiation, de novo initiation, rna virus, bvdv, bovine viral diarrhea virus, replication, rna binding protein
• Biological source: Bovine viral diarrhea virus 1
• Cellular location: E(rns) glycoprotein: Host membrane; Peripheral membrane protein. Envelope glycoprotein E2: Host cell surface. Cysteine protease NS2: Host membrane; Multi- pass membrane protein (Potential): P19711
• Total number of polymer chains: 1
• Total formula weight: 70490.74

Authors

Choi, K.H.,Groarke, J.M.,Young, D.C.,Kuhn, R.J.,Smith, J.L.,Pevear, D.C.,Rossmann, M.G. (deposition date: 2004-01-15, release date: 2004-04-06, Last modification date: 2024-11-13)

Primary citation

Choi, K.H.,Groarke, J.M.,Young, D.C.,Kuhn, R.J.,Smith, J.L.,Pevear, D.C.,Rossmann, M.G.
The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation.
Proc.Natl.Acad.Sci.Usa, 101:4425-4430, 2004

PubMed Abstract: The bovine viral diarrhea virus (BVDV) RNA-dependent RNA polymerase can initiate RNA replication by a de novo mechanism without a primer. The structure of BVDV polymerase, determined to 2.9-A resolution, contains a unique N-terminal domain, in addition to the fingers, palm, and thumb domains common to other polymerases. The structure of BVDV polymerase complexed with GTP, which is required for de novo (primer-independent) initiation, shows that GTP binds adjacent to the initiation NTP, suggesting that the GTP mimics a vestigial RNA product. Comparison of five monomers in two different crystal forms showed conformational changes in the fingertip region and in the thumb domain that may help to translocate the RNA template and product strands during elongation. The putative binding sites of previously reported BVDV inhibitors are also discussed.

PubMed: 15070734
DOI: 10.1073/pnas.0400660101

Experimental method

X-RAY DIFFRACTION (3 Å)