4HDH

Crystal Structure of viral RdRp in complex with ATP

Summary for 4HDH

• Entry DOI: 10.2210/pdb4hdh/pdb
• Related: 4HDG
• Descriptor: Polyprotein, ADENOSINE-5'-TRIPHOSPHATE, ZINC ION, ... (4 entities in total)
• Functional Keywords: dna/rna polymerases, rna directed rna polymerase, transferase
• Biological source: Japanese encephalitis virus
• Cellular location: Virion membrane; Multi-pass membrane protein: G3LHD9
• Total number of polymer chains: 2
• Total formula weight: 148045.14

Authors

Surana, P.,Nair, D.T. (deposition date: 2012-10-02, release date: 2013-12-25, Last modification date: 2023-09-20)

Primary citation

Surana, P.,Satchidanandam, V.,Nair, D.T.
RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state.
Nucleic Acids Res., 42:2758-2773, 2014

PubMed Abstract: Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5'-CU-3' at the 3'-end of the flaviviral genome is highly conserved. Surprisingly, flaviviral RdRps require high concentrations of the second incoming nucleotide GTP to catalyze de novo template-dependent RNA synthesis. We show that GTP stimulates de novo RNA synthesis by RdRp from Japanese encephalitis virus (jRdRp) also. Crystal structures of jRdRp complexed with GTP and ATP provide a basis for specific recognition of GTP. Comparison of the jRdRpGTP structure with other viral RdRp-GTP structures shows that GTP binds jRdRp in a novel conformation. Apo-jRdRp structure suggests that the conserved motif F of jRdRp occupies multiple conformations in absence of GTP. Motif F becomes ordered on GTP binding and occludes the nucleotide triphosphate entry tunnel. Mutational analysis of key residues that interact with GTP evinces that the jRdRpGTP structure represents a novel pre-initiation state. Also, binding studies show that GTP binding reduces affinity of RdRp for RNA, but the presence of the catalytic Mn(2+) ion abolishes this inhibition. Collectively, these observations suggest that the observed pre-initiation state may serve as a checkpoint to prevent erroneous template-independent RNA synthesis by jRdRp during initiation.

PubMed: 24293643
DOI: 10.1093/nar/gkt1106

Experimental method

X-RAY DIFFRACTION (2.28 Å)