2KQV

SARS coronavirus-unique domain (SUD): Three-domain molecular architecture in solution and RNA binding. I: Structure of the SUD-M domain of SUD-MC

Summary for 2KQV

• Entry DOI: 10.2210/pdb2kqv/pdb
• Related: 2KQW
• Descriptor: Non-structural protein 3 (1 entity in total)
• Functional Keywords: severe acute respiratory syndrome (sars), nonstructural protein 3, macrodomains, rna-binding proteins, structural genomics, psi-2, jcsg, functional and structural proteomics of the sars coronavirus, protein structure initiative, joint center for structural genomics, viral protein
• Biological source: SARS coronavirus
• Cellular location: Non-structural protein 3: Host membrane; Multi-pass membrane protein (Potential). Non-structural protein 4: Host membrane; Multi-pass membrane protein (Potential). Non-structural protein 6: Host membrane; Multi-pass membrane protein (Potential). Non-structural protein 7: Host cytoplasm, host perinuclear region (By similarity). Non-structural protein 8: Host cytoplasm, host perinuclear region (By similarity). Non-structural protein 9: Host cytoplasm, host perinuclear region (By similarity). Non-structural protein 10: Host cytoplasm, host perinuclear region (By similarity): P0C6U8
• Total number of polymer chains: 1
• Total formula weight: 22205.43

Authors

Johnson, M.A.,Chatterjee, A.,Wuthrich, K.,Joint Center for Structural Genomics (JCSG) (deposition date: 2009-11-19, release date: 2009-12-22, Last modification date: 2024-05-22)

Primary citation

Johnson, M.A.,Chatterjee, A.,Neuman, B.W.,Wuthrich, K.
SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding.
J.Mol.Biol., 400:724-742, 2010

PubMed Abstract: Nonstructural protein 3 of the severe acute respiratory syndrome (SARS) coronavirus includes a "SARS-unique domain" (SUD) consisting of three globular domains separated by short linker peptide segments. This work reports NMR structure determinations of the C-terminal domain (SUD-C) and a two-domain construct (SUD-MC) containing the middle domain (SUD-M) and the C-terminal domain, and NMR data on the conformational states of the N-terminal domain (SUD-N) and the SUD-NM two-domain construct. Both SUD-N and SUD-NM are monomeric and globular in solution; in SUD-NM, there is high mobility in the two-residue interdomain linking sequence, with no preferred relative orientation of the two domains. SUD-C adopts a frataxin like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. The structures of both SUD-M (previously determined) and SUD-C (from the present study) are maintained in SUD-MC, where the two domains are flexibly linked. Gel-shift experiments showed that both SUD-C and SUD-MC bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases, whereby SUD-MC binds to a more restricted set of purine-containing RNA sequences than SUD-M. NMR chemical shift perturbation experiments with observations of (15)N-labeled proteins further resulted in delineation of RNA binding sites (i.e., in SUD-M, a positively charged surface area with a pronounced cavity, and in SUD-C, several residues of an anti-parallel beta-sheet). Overall, the present data provide evidence for molecular mechanisms involving the concerted actions of SUD-M and SUD-C, which result in specific RNA binding that might be unique to the SUD and, thus, to the SARS coronavirus.

PubMed: 20493876
DOI: 10.1016/j.jmb.2010.05.027

Experimental method

SOLUTION NMR