2LNC

Solution NMR structure of Norwalk virus protease

Summary for 2LNC

• Entry DOI: 10.2210/pdb2lnc/pdb
• NMR Information: BMRB: 17523
• Descriptor: 3C-like protease (1 entity in total)
• Functional Keywords: viral protease, chymotrypsin-like protease, hydrolase, calicivirus
• Biological source: Norovirus
• Cellular location: Protein p48: Host membrane; Single-pass membrane protein (Potential). NTPase: Host membrane; Single-pass membrane protein (Potential). Protein p22: Host membrane; Single-pass membrane protein (Potential): Q83883
• Total number of polymer chains: 1
• Total formula weight: 20126.13

Authors

Takahashi, D.,Hiromasa, Y.,Kim, Y.,Anbanandam, A.,Chang, K.,Prakash, O. (deposition date: 2011-12-22, release date: 2012-12-26, Last modification date: 2024-05-01)

Primary citation

Takahashi, D.,Hiromasa, Y.,Kim, Y.,Anbanandam, A.,Yao, X.,Chang, K.O.,Prakash, O.
Structural and dynamics characterization of norovirus protease.
Protein Sci., 22:347-357, 2013

PubMed Abstract: Norovirus protease is an essential enzyme for proteolytic maturation of norovirus nonstructural proteins and has been implicated as a potential target for antiviral drug development. Although X-ray structural studies of the protease give us wealth of structural information including interactions of the protease with its substrate and dimeric overall structure, the role of protein dynamics in the substrate recognition and the biological relevance of the protease dimer remain unclear. Here we determined the solution NMR structure of the 3C-like protease from Norwalk virus (NV 3CLpro), a prototype strain of norovirus, and analyzed its backbone dynamics and hydrodynamic behavior in solution. ¹⁵N spin relaxation and analytical ultracentrifugation analyses demonstrate that NV 3CLpro is predominantly a monomer in solution. Solution structure of NV 3CLpro shows significant structural variation in C-terminal domain compared with crystal structures and among lower energy structure ensembles. Also, ¹⁵N spin relaxation and Carr-Purcell-Meiboom-Gill (CPMG)-based relaxation dispersion analyses reveal the dynamic properties of residues in the C-terminal domain over a wide range of timescales. In particular, the long loop spanning residues T123-G133 show fast motion (ps-ns), and the residues in the bII-cII region forming the large hydrophobic pocket (S2 site) undergo conformational exchanges on slower timescales (μs-ms), suggesting their important role in substrate recognition.

PubMed: 23319456
DOI: 10.1002/pro.2215

Experimental method

SOLUTION NMR