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3d02

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

    Title Crystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution. To be published
    Site JCSG
    PDB Id 3d02 Target Id 390056
    Molecular Characteristics
    Source Klebsiella pneumoniae subsp. pneumoniae mgh 78578
    Alias Ids TPS1783,YP_001338366.1, 283042 Molecular Weight 32937.92 Da.
    Residues 302 Isoelectric Point 6.13
    Sequence aaektvvniskvdgmpwfnrmgegvvqagkefnlnasqvgpsstdapqqvkiiedliarkvdaitivpn danvlepvfkkardagivvltnespgqpsanwdveiidnekfaaeyvehmakrmggkggyviyvgsltv pqhnlwadllvkyqkehypdmhevtrrmpvaesvddsrrttldlmktypdlkavvsfgsngpigagrav kekraknkvavygmmipsqaasliksgditegitydpatagyalaavastllngktiepgfelkelgka evdsdkhiirfhkvllvnkdnidsly
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.30 Rfree 0.172
    Matthews' coefficent 2.17 Rfactor 0.157
    Waters 316 Solvent Content 43.33

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3d02
    1. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    H Van Den Bedem, A Dhanik, JC Latombe - Section D: Biological , 2009 - scripts.iucr.org
     
    2. Investigation of cation interactions in sugar-binding proteins
    P Elumalai, M Rajasekaran, HL Liu, C Chen - Protoplasma, 2010 - Springer
     
    3. 3 ___________
    H Laga_ ____ - ___________, 2009 - J-STAGE
     

    Protein Summary

    Protein KPN_04753 (accession number YP_001338366.1 , gi number 152973220, Refsec  NC_009648.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 is a very divergent member of the type-1 periplasmic binding protein family (SCOP family 93.1.1, PFAM clan Periplas_BP-like (CL0144)).  This homology is not recognized by PFAM HMM, but has a strong statistical significance in Fold & Function Assignment System (FFAS), and is supported by the strong structuraly similar to proteins from this family, such as  1BA2, 1TJY and 1GUB. A conserved binding site has been found in the interface between two domains.  One glycerol molecule from crystallization has been modeling in the active site, which is an analogue to the open form of D-xylose. Both SEC data and interaction interface calculation suggest the biomolecule of protein KPN_04753  is a monomer.  

     

     

    Figure 1. The structure of KPN_04753 protein consists of two intertwinned domains. One Glycerol molecule from cryoprotectant has been modeled on the interface between two domains

     

     

    Figure 2. The structure of KPN_04753 protein carries a "HOLO" conformation since glycerol can be regarded as an analogue of the open-form D-xylose in the conserved active site.

     

     

    Figure 3. The direct structural superposion between the structure of KPN_04753 protein and Salmonella typhimurium AI-2 receptor LsrB (PDB 1TJY) supports its homology to 1TJY and other proteins from this family.

     

     

    Figure 4. A glycerol molecule from cryoprotectant is modeled in the conserved acitve site of protein  YP_001338366.1, which can be regarded as a structural analogue to the open -form of D-xylose at the conserved active site.

     

    Ligand Summary

    Glycerol molecule, Cl- ions


    References

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