2QEQ

Crystal structure of kunjin virus ns3 helicase

Summary for 2QEQ

• Entry DOI: 10.2210/pdb2qeq/pdb
• Descriptor: Flavivirin protease NS3 catalytic subunit (1 entity in total)
• Functional Keywords: helicase; flavivirus, hydrolase
• Biological source: Kunjin virus (STRAIN MRM61C)
• Cellular location: Capsid protein C: Virion (Potential). Peptide pr: Secreted (By similarity). Small envelope protein M: Virion membrane; Multi-pass membrane protein (By similarity). Envelope protein E: Virion membrane; Multi- pass membrane protein (By similarity). Non-structural protein 1: Secreted. Non-structural protein 2A: Host endoplasmic reticulum membrane; Multi-pass membrane protein (Potential). Serine protease subunit NS2B: Host endoplasmic reticulum membrane; Multi-pass membrane protein (Potential). Serine protease NS3: Host endoplasmic reticulum membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Non-structural protein 4A: Host endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity). Non-structural protein 4B: Host endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity). RNA-directed RNA polymerase NS5: Host endoplasmic reticulum membrane; Peripheral membrane protein; Cytoplasmic side (By similarity): P14335
• Total number of polymer chains: 2
• Total formula weight: 98022.99

Authors

Milani, M.,Mastrangelo, E.,Bolognesi, M. (deposition date: 2007-06-26, release date: 2007-08-14, Last modification date: 2023-08-30)

Primary citation

Mastrangelo, E.,Milani, M.,Bollati, M.,Selisko, B.,Peyrane, F.,Pandini, V.,Sorrentino, G.,Canard, B.,Konarev, P.V.,Svergun, D.I.,de Lamballerie, X.,Coutard, B.,Khromykh, A.A.,Bolognesi, M.
Crystal structure and activity of Kunjin virus NS3 helicase; protease and helicase domain assembly in the full length NS3 protein
J.Mol.Biol., 372:444-455, 2007

PubMed Abstract: Flaviviral NS3 is a multifunctional protein displaying N-terminal protease activity in addition to C-terminal helicase, nucleoside 5'-triphosphatase (NTPase), and 5'-terminal RNA triphosphatase (RTPase) activities. NS3 is held to support the separation of RNA daughter and template strands during viral replication. In addition, NS3 assists the initiation of replication by unwinding the RNA secondary structure in the 3' non-translated region (NTR). We report here the three-dimensional structure (at 3.1 A resolution) of the NS3 helicase domain (residues 186-619; NS3:186-619) from Kunjin virus, an Australian variant of the West Nile virus. As for homologous helicases, NS3:186-619 is composed of three domains, two of which are structurally related and held to host the NTPase and RTPase active sites. The third domain (C-terminal) is involved in RNA binding/recognition. The NS3:186-619 construct occurs as a dimer in solution and in the crystals. We show that NS3:186-619 displays both ATPase and RTPase activities, that it can unwind a double-stranded RNA substrate, being however inactive on a double-stranded DNA substrate. Analysis of different constructs shows that full length NS3 displays increased helicase activity, suggesting that the protease domain plays an assisting role in the RNA unwinding process. The structural interaction between the helicase and protease domain has been assessed using small angle X-ray scattering on full length NS3, disclosing that the protease and helicase domains build a rather elongated molecular assembly differing from that observed in the NS3 protein from hepatitis C virus.

PubMed: 17658551
DOI: 10.1016/j.jmb.2007.06.055

Experimental method

X-RAY DIFFRACTION (3.1 Å)