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The Open Protein Structure Annotation Network
PDB Keyword
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2kqv

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

    Title SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding. J.Mol.Biol. 400 724-742 2010
    Site JCSG
    PDB Id 2kqv Target Id 416489
    Related PDB Ids 2kqw 
    Molecular Characteristics
    Source Sars coronavirus
    Alias Ids TPS31058,NP_828850.1 Molecular Weight 21763.81 Da.
    Residues 194 Isoelectric Point 6.59
    Sequence gtvswnlremlahaeetrklmpicmdvraimatiqrkykgikiqegivdygvrfffytskepvasiitk lnslneplvtmpigyvthgfnleeaarcmrslkapavvsvsspdavttyngyltsssktseehfvetvs lagsyrdwsysgqrtelgveflkrgdkivyhtlespvefhldgevlsldklkslls
      BLAST   FFAS

    Structure Determination
    Method NMR Chains 1

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2kqv
    1. SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding
    MA Johnson, A Chatterjee, BW Neuman - Journal of molecular , 2010 - Elsevier
     

    Protein Summary

    The gene NP_828850.1 from Sars coronavirus encodes a central segment of the SARS-unique domain (SUD-M, for "middle of the SARS-unique domain") in the nonstructural protein Nsp3, that belongs to the group PF11633.  SUD-M(513-651) exhibits a macrodomain fold containing the Nsp3 residues 528 to 648, and there is an extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail with residues 649 to 651.  NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) RNA.  

    Pre-SCOP classifies 2kqw in the alpha/beta class, macro domain-like (super)family. Dali significant hits (Z-scr=10) are with 3ejg, 2acf and 2dx6.

    SUD-M(527-651) has the closest three-dimensional structure similarity with another domain of Nsp3, the ADP-ribose-1"-phosphatase Nsp3b, 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, but it does not contain the motifs of catalytic residues found in these structural homologues [Ref].  The Nudix fold type classification SCOP55811 is in agreement with these observations, suggesting Nudix hydrolase-like functionality.  Nudix hydrolases are found in all classes of organisms and hydrolyse a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, dinucleoside and diphosphoinositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity [Ref].

    Ligand Summary

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