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

    Title The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold. Acta Crystallogr.,Sect.F 66 1254-1260 2010
    Site JCSG
    PDB Id 3f1z Target Id 390051
    Molecular Characteristics
    Source Klebsiella pneumoniae subsp. pneumoniae mgh 78578
    Alias Ids TPS7664,YP_001337197.1, 91415 Molecular Weight 14432.56 Da.
    Residues 132 Isoelectric Point 9.40
    Sequence askafysagdklfqpgddavasmqtysvaqflqpftlnpakassdylgkwvkvrgvivdirrksgiags yyfivtmrdeqnktdkrltfnfgshnsadvealsngsvativgqvhqvqdstiptlqnpkvvk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 10
    Resolution (Å) 2.46 Rfree 0.228
    Matthews' coefficent 3.19 Rfactor 0.192
    Waters 325 Solvent Content 61.44

    Ligand Information


    Google Scholar output for 3f1z
    1. The structure of KPN03535 (gi| 152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold
    D Das, P Kozbial, GW Han, D Carlton - Section F: Structural , 2009 - scripts.iucr.org
    2. New variants of known folds: do they bring new biology?
    EV Koonin - Acta Crystallographica Section F: Structural Biology , 2010 - scripts.iucr.org

    Protein Summary

    Note: This structure has been accepted for publication in ActaF. Detailed structural analysis is presented in that manuscript which is in press, as of April 2010.

    Pfam update: This is a family of bacterial, archeael and viral proteins that is related to the tRNA_anti family Pfam:PF01336. The major characteristic of families like tRNA_anti is their OB-fold, and many of them bind DNA. and found, after a couple of rounds of iteration, one overlap to tRNA_anti, so went on and found more; so I have put it into the OB_-fold clan.

    This protein appears to be very novel in sequence. PSI-BLAST does not return significant hits with any other sequence. It does not have any PfamA annotation yet but a search against PfamA shows weak similarity (exp=0.71) to the family tRNA_anti PF01336 which contains proteins with the OB-fold/nucleic acid binding domain.

    FFAS also does not show any significant hits.

    The protein sequence has a predicted signal sequence which was removed during the gene construct design. The cloned construct comprises amino acids 23-145 of the full-length protein from 1-145.

    There are 10 protomers in the asymmetric unit of the crystal lattice. They form a dimer of a stacked pentameric ring:


    However, crystal packing analysis using the PISA server does not indicate that this decameric structure is stable in solution and the prediction for solution state is a monomer. Size exclusion chromatography coupled with static light scattering (SEC/SLS) also indicate a monomer as the oligomeric form in solution. So it is rather interesting to see this assembly in the crystal structure.

    The structure of the monomer resembles that of an OB-fold:


     A search for proteins of similar structure using SSM at EBI shows the top hits (although Q-score is < 0.5) to the Shiga toxin protein and Human RepA (a single-stranded DNA binding protein with OB-fold). The Shiga toxin can also form a pentameric ring, but the diameter of the Shiga toxin ring is much smaller than the diameter of the pentamer that is observed here (~36 Angstroms). A search of similar structures using DALI shows some similarity to the aspartyl-tRNA synthetases anticodon domain which belongs to the PFam listed above.

    Further analysis of this structure will be made to understand possible structure-function relationships.


    KPN_03535 is predicted lipoprotein with SPaseII-cleaved signal peptide. This part was contributed by Piotr Kozbial.

    Prediction of lipoprotein signal peptides by LipoP-1.0 server [Juncker et al 2003, http://www.cbs.dtu.dk/services/LipoP-1.0/] supports twilight zone protein sequence similarity of KPN_03535 (GenBank: YP_001337197) to bacterial lipoproteins. The predicted cleavage site by LipoP-1.0 server (score: 17.664) is located before Cys-20 (SLLSG^CGLAS). The further analysis of this putative lipoprotein will answer the question if KPN_03535 belongs to known bacterial lipoproteins or has a completely new function.


    There is only one known homolog of KPN_03535 that is annotated as predicted lipoprotein (KPK_0575, GenBank: ACI09130.1, Klebsiella pneumoniae 342). KPK_0575 is encoded next to its genomic neighbour KPK_0576 (it is also annotated as putative lipoprotein) but on the opposite strand. Detailed analysis should reveal whether KPK_0575 and KPK_0576 are expressed and what regulate their expression (to do: see if the expression of one of them is inhibiting expression of the other one)

    Ligand Summary




    No references found.

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