2KAF
Solution structure of the SARS-unique domain-C from the nonstructural protein 3 (nsp3) of the severe acute respiratory syndrome coronavirus
Summary for 2KAF
| Entry DOI | 10.2210/pdb2kaf/pdb |
| Descriptor | Non-structural protein 3 (1 entity in total) |
| Functional Keywords | sars coronavirus, nonstructural protein 3, sars-unique domain-c, automation in nmr structure determination, viral protein, hydrolase. joint center for structural genomics. jcsg. psi, protein structure initiative, rna binding protein |
| Biological source | SARS coronavirus (SARS-CoV) |
| 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 | 7596.43 |
| Authors | Johnson, M.A.,Mohanty, B.,Pedrini, B.,Serrano, P.,Chatterjee, A.,Herrmann, T.,Joseph, J.,Saikatendu, K.,Wilson, I.A.,Buchmeier, M.J.,Kuhn, P.,Wuthrich, K.,Joint Center for Structural Genomics (JCSG) (deposition date: 2008-11-05, release date: 2008-11-25, Last modification date: 2024-05-01) |
| 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 Cited by 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: 20493876DOI: 10.1016/j.jmb.2010.05.027 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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