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The Open Protein Structure Annotation Network
PDB Keyword
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4qgp

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

    Title Crystal structure of a pyrophosphatase (AF1178) from Archaeoglobus fulgidus DSM 4304 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 4qgp Target Id 356701
    Molecular Characteristics
    Source Archaeoglobus fulgidus dsm 4304
    Alias Ids TPS2451,NP_070007.1, 282911 Molecular Weight 12753.96 Da.
    Residues 106 Isoelectric Point 4.95
    Sequence meelldilrefrdsrgwlkyhtpknlavsisievaelleifqwtrssdeefevlerrkgeveeeiadvl iyllflcdvaeinpieavkrkmeknerkypknrvhef
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.78 Rfree 0.2380
    Matthews' coefficent 2.25 Rfactor 0.1935
    Waters 106 Solvent Content 45.45

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Target ID 356701 belongs to the MazG(PF03819) Pfam family. Members of this Pfam family are associated with nucleotide pyrophosphorylase activity and ~40 structures have been determined for this Pfam family. Shown below is a ribbons representation of the monomeric structure of target ID 356701 color coded with the N-terminal end in blue and the C-terminal end in red,

    monomer.png

     

     The structure of target ID 356701 is similar to those belonging to the all-alpha NTP pyrophosphotases SCOP fold. The structures in this SCOP fold are multi-helical consisting of a dimeric four alpha-helical bundle that oligomerizes further into a tetramer. The EBI/PISA server predicts from the crystal structure that both the dimer and tetramer are possible oligomeric. The structuire indicates that the stacking of the imidazole sidechains belonging to two different polypeptide chains stabilizes the dimer. Shown below is a ribbons representation of the predicted dimer with the sidechains in green and yellow. The sidechains of the His residues in the N-terminal tag are also depicted.

    histag_stacking.png

     

     The crystal structure suggests these individual dimers aggregate to form a tetramer shown below:

     

    tetramer.png

     

     

    PDB ID
    DALI Z-Score
    rmsd (Ang)
    length of alignment
    total residue in PDB ID
    sequence ID (%)
    Title
    Citation
    2a3q_B 11.2 2.3 101 109 31 X-Ray Structure of Protein from Mus Musculus MM.29898 Center for Eukaryotic Structural Genomics
    2oie_B 11.0 2.4 96 109 30 Crystal structure of RS21-C6 core segment RSCUT [Ref]
    2oig_A 10.8 2.3 95 104 32 Crystal structure of RS21-C6 core segment and dm5CTP complex
     
    [Ref]
    2q4p_B 10.3 2.5 101 109 32

    Ensemble refinement of the crystal structure of protein from Mus musculus Mm.29898

     
    [Ref]
    2gta_C 9.9 2.6 85 86 25 Crystal Structure of the putative pyrophosphatase YPJD from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR428.  
    1vmg_A 8.4 2.8 79 83 23 Crystal structure of MazG nucleotide pyrophosphohydrolase (13816655) from Sulfolobus solfataricus at 1.46 A resolution JCSG
    1yvw_A 8.3 3.6 83 92 20 Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus. NESGC target BcR13.  
    2q5z_A 7.9 4.0 84 93 29 Crystal structure of iMazG from Vibrio DAT 722: Ntag-iMazG (P43212) [Ref]
    3crc_A 7.8 2.8 87 225 24 Crystal Structure of Escherichia coli MazG, the Regulator of Nutritional Stress Response [Ref]

     

     

     

    Ligand Summary

    Reviews

    References

     

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