5TSN

Crystal structures of Norwalk virus polymerase bound to an RNA primer-template duplex

Summary for 5TSN

• Entry DOI: 10.2210/pdb5tsn/pdb
• Descriptor: Norwalk virus polymerase, RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'), MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: norwalk virus, rna dependent rna polymerase, rna primer-template complex, transferase-rna complex, transferase/rna
• Biological source: Norwalk virus; More
• Total number of polymer chains: 3
• Total formula weight: 62036.60

Authors

Shaik, M.M.,Ng, K.K. (deposition date: 2016-10-30, release date: 2017-04-12, Last modification date: 2023-10-04)

Primary citation

Shaik, M.M.,Bhattacharjee, N.,Feliks, M.,Ng, K.K.,Field, M.J.
Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences.
Proteins, 85:1435-1445, 2017

PubMed Abstract: Norovirus (NV) RNA-dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer-template duplex was investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the post-incorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435-1445. © 2017 Wiley Periodicals, Inc.

PubMed: 28383118
DOI: 10.1002/prot.25304

Experimental method

X-RAY DIFFRACTION (2.1 Å)