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3db7

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

    Title Crystal structure of putative calcium-regulated periplasmic protein of unknown function (NP_809836.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.40 A resolution. To be Published
    Site JCSG
    PDB Id 3db7 Target Id 389981
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS7646,NP_809836.1, 87681 Molecular Weight 14617.92 Da.
    Residues 126 Isoelectric Point 5.71
    Sequence adddkpiqvtqmpqlaqqfikqhfsdskvalakmesdflyksyeviftngnkvefdkkgnweevdckht svpvaiipaaiqkyvttnypdakvlkierdkkdyevklsnrtelkfdlkfnlididn
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.40 Rfree 0.19824
    Matthews' coefficent 2.22 Rfactor 0.16034
    Waters 197 Solvent Content 44.58

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3db7
    1. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families
    K Ellrott, L Jaroszewski, W Li, JC Wooley - PLoS computational , 2010 - dx.plos.org
     
    2. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    3. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function
    D Das, RD Finn, D Carlton, MD Miller - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Gene BT0923 from Bacteroides thetaiotaomicron vpi-5482 encodes the NP_809836 protein, showing a tandem repeat of the DUF2874 sequence (PF11396). This putative calcium-regulated periplasmic protein of unknown function (BT0923) may be functionally associated with its genomic neighbors: BT0922 (putative lipoprotein) and BT0924 (predicted membrane protein). Pre-SCOP classifies 3db7 in the alpha+beta class, BLIP-like fold, BT0923-like (super)family. DALI structural similarity search top hits using 3db7 as query are with PDB:3due (Z=23) and PDB:3elg (Z=20).
     
    NP_809836 structure, 3db7, has an overall beta-saddle fold consisting of two tandem repeats. Three Ca2+ ions from the crystallization condition have been modeled in the structure. There is one
    NP_809836 molecule in each asymmetric unit. According to the results from size exclusion chromatography with static light scattering, the biomolecule of NP_809836 should be a monomer as a significant oligomerization state. Interestingly, the surface interaction calculation (PISA) predicts that the NP_809836 molecule will also be a monomer in the solution if there is no Ca2+ included in the structure. With two of these three Ca2+ in the structure, PISA suggests the NP_809836 in the solution can be "glued" as a stable dimer as the probable quaternary structure. The total buried surface area from complex between two NP_809836 molecules is 2450 Å2. The experimental results from size exclusion chromatography with static light scattering(SEC+SLS), without adding Ca ion, supports the assignment of a monomer as a signficant oligomerization state in solution.  When a sample was run with 0.2 M Calcium Chloride in the mobile phase (similar concentration to that in the crystallization reagent), the SEC+SLS results showed primarily dimer.  In this dimer structure, Glu 63, 73 and 82, Asp 142, Asp 144, 1ILE 143 in NP_809836 are involved in the Ca2+ complexing.

    A simple "docking" via directly structural superposing comparison between this structure to the coresponding subunit in the complex structure of  β-lactamase inhibitor protein-II/TEM-1 β-lactamase complex reveals that Glu 63, 73, 82 in current model are important for Ca "glueing" to the carbonyl group of Pro 107 and Glu110 side chain from the TEM-1 beta-lactamase in the structure of β-lactamase inhibitor protein-II/TEM-1 β-lactamase complex structure (PDB ID: 1JTG). 

     

    More details will be released.


     

    Figure 1   NP_809836 molecule complexed with two of three

    Ca2+ has an overall beta-saddle fold consisting of two tandem repeats.

     

    Figure 2   Another view of NP_809836 molecule .

     

     

    Figure 3   Two NP_809836 molecules form a stable dimer

    through two Ca cations.

     

    Figure 4 Glu 63, 73, 82 from one NP_809836 molecule and Asp 142, Asp144,

    ILE143 from another NP_809836 molecule  participates in the complex formation with 2 Ca2+.

    Ligand Summary

    Ca2+, Ethlyene Glycol

    Reviews

    References

     

    No references found.

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