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PDBsum entry 2kaf
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Viral protein, RNA binding protein
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PDB id
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2kaf
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References listed in PDB file
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Key reference
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Title
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Sars coronavirus unique domain: three-Domain molecular architecture in solution and RNA binding.
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Authors
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M.A.Johnson,
A.Chatterjee,
B.W.Neuman,
K.Wüthrich.
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Ref.
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J Mol Biol, 2010,
400,
724-742.
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PubMed id
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Abstract
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The nonstructural protein 3 (nsp3) of the severe acute respiratory syndrome
coronavirus (SARS-CoV) includes a "SARS-unique region" (SUD) consisting of three
globular domains separated by short linker peptide segments. This paper reports
NMR structure determinations of the C-terminal domain (SUD-C) and of 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, and 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 observation of the (15)N-labeled
proteins further resulted in the delineation of the 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 antiparallel beta-sheet. Overall, the present data
provide evidence for molecular mechanisms involving 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-CoV.
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