3DDK

Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase

Summary for 3DDK

• Entry DOI: 10.2210/pdb3ddk/pdb
• Descriptor: RNA polymerase B3 3Dpol, SODIUM ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: rna polymerase, viral polymerase, rna virus, transferase, viral protein
• Biological source: Human coxsackievirus
• Cellular location: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . Virion : Q66338
• Total number of polymer chains: 1
• Total formula weight: 53260.33

Authors

Campagnola, G.,Weygandt, M.H.,Scoggin, K.E.,Peersen, O.B. (deposition date: 2008-06-05, release date: 2008-09-23, Last modification date: 2023-08-30)

Primary citation

Campagnola, G.,Weygandt, M.H.,Scoggin, K.E.,Peersen, O.B.
Crystal Structure of Coxsackievirus B3 3Dpol Highlights Functional Importance of Residue 5 in Picornaviral Polymerases
J.Virol., 82:9458-9464, 2008

PubMed Abstract: The crystal structure of the coxsackievirus B3 polymerase has been solved at 2.25-A resolution and is shown to be highly homologous to polymerases from poliovirus, rhinovirus, and foot-and-mouth disease viruses. Together, these structures highlight several conserved structural elements in picornaviral polymerases, including a proteolytic activation-dependent N-terminal structure that is essential for full activity. Interestingly, a comparison of all of the picornaviral polymerase structures shows an unusual conformation for residue 5, which is always located at a distortion in the beta-strand composed of residues 1 to 8. In our earlier structure of the poliovirus polymerase, we attributed this conformation to a crystal packing artifact, but the observation that this conformation is conserved among picornaviruses led us to examine the role of this residue in further detail. Here we use coxsackievirus polymerase to show that elongation activity correlates with the hydrophobicity of residue 5 and, surprisingly, more hydrophobic residues result in higher activity. Based on structural analysis, we propose that this residue becomes buried during the nucleotide repositioning step that occurs prior to phosphoryl transfer. We present a model in which the buried N terminus observed in all picornaviral polymerases is essential for stabilizing the structure during this conformational change.

PubMed: 18632862
DOI: 10.1128/JVI.00647-08

Experimental method

X-RAY DIFFRACTION (2.25 Å)