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2qtp

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

    Title Crystal structure of protein of unknown function (DUF1185) (YP_166079.1) from Silicibacter pomeroyi DSS-3 at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 2qtp Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1630,YP_166079.1, PF06684, 383054
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.54 Rfactor 0.204
    Waters
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    Solvent Content 51.60

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2qtp
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    2. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-
    C Bakolitsa, A Kumar, KK Jin, D McMullan - Section F: Structural , 2010 - scripts.iucr.org
     

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    Protein Summary

    The SPO0826 gene encodes the YP_166079 amino acid sequence that belongs to the DUF1185 group (PF06684). This protein family contains more than 200 sequence homologs found mostly in proteobacteria, but found also in Firmicutes and uncultured bacteria from ocean, soil, and human microbiomes, all of which are around 180 residues in length. Members of the DUF1185 family are also present in several human and animal pathogens from the Burkholderia and Bordetella, as well as Clostridia, groups, where their genome location on virulence islands suggests a possible role in pathogenesis (1).

    The genomic neighborhood of SPO0826 and its orthologs, includes proteins implicated in ABC-type branched-chain amino acid transport and ABC transporter genes, suggesting that the principal products are secreted. One possibility would involve the DUF1185(PF06684) family in the production of nonribosomal peptides, which in microorganisms act as iron-acquisition siderophores, antibiotics, and toxins involved in pathogenesis. ZP_05780371, with 47% sequence identity to YP_166079, is annotated as peptide synthase.

    SCOP classifies 2qtp in the alpha+beta class, Bacillus chorismate mutase-like fold, BB2672-like (super)family. SPO0826 and BB2672 are closely homologous with a sequence identity of 39% and share the same overall fold and tertiary structure. Structural superposition between the two structures extends over 142 C-alpha atoms from each domain with an RMSD of 1.4 Å, and a DALI Z-score of 20  (Fig. 1). The residues missing from the SPO0826 structure correspond to regions implicated in the formation of the biologically relevant hexamer. See 3byq entry for more details.



    Figure 1. Stereo ribbon diagram of a superposition of BB2672 (grey, PDB: 3byq) and SPO0826 (blue, PDB: 2qtp).

    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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