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2rnk

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold. J.Virol. 83 1823-1836 2009
    Site JCSG
    PDB Id 2rnk Target Id 388820
    Related PDB Ids 2jzf 
    Molecular Characteristics
    Source Sars coronavirus tor2
    Alias Ids TPS9380,29837497 Molecular Weight 15428.09 Da.
    Residues 139 Isoelectric Point 7.93
    Sequence vlpseapnakeeilgtvswnlremlahaeetrklmpicmdvraimatiqrkykgikiqegivdygvrff fytskepvasiitklnslneplvtmpigyvthgfnleeaarcmrslkapavvsvsspdavttyngyltss
      BLAST   FFAS

    Structure Determination
    Method NMR Chains 1

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2rnk
    1. Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold
    A Chatterjee, MA Johnson, P Serrano, B Pedrini - Journal of , 2009 - Am Soc Microbiol
     

    Protein Summary

    The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. This domain belongs to the Nsp3 family (PF11633). NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1"-phosphatase nsp3b (PDB_ID: 3EWQ; Z=10), although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins (3KH6; Z=8), but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

    Ligand Summary

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