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The Open Protein Structure Annotation Network
PDB Keyword
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3kzt

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

    Title Crystal structure of Protein of unknown function (NP_812423.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 3kzt Target Id 392985
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20275,NP_812423.1, 324890 Molecular Weight 15837.71 Da.
    Residues 142 Isoelectric Point 4.35
    Sequence knmdtsaepadvqanvsdssrieqeaigmiedfyeayaasfmstgkealalgdsikqkfltkeliekvd rlieatdadpiiraqdlgendmktlsvkhlndnwyevnytsakgsqyeravsipvrvvnvdgqyliddi tpen
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.10 Rfree 0.268
    Matthews' coefficent 2.05 Rfactor 0.222
    Waters 118 Solvent Content 39.97

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Protein BT_3511 (JCSG target ID 392985, JCSG target accession code GS13395A, GenBank accession code NP_812423.1) is a 167-residue long protein from Bacteriodes thetaiotaomicron, a gram-negative bacterium that is a prevalent member of the human intestinal flora.

    The protein belongs to Pfam DUF3828, of which this is the first structure.  The structure of N-terminally truncated BT_3511 (residues 26-167), solved by Se-MAD to a resolution of 2.1 Angstroms, adopts an alpha-beta structure that belongs to the NTF2-like superfamily in the SCOP classification scheme (Figures 1ab).

    Figure 1. Structure of a monomer of BT_3511 (a) gradiently colored from the N- (blue) to the C-terminus (red) and (b) colored by secondary structural elements (helices in blue, beta strands in red, loops in yellow).

    (a)                                                                (b)

    GS13395A-gradient.png             GS13395A-ss.png

    Analytical size exclusion chromatography (anSEC), crystal packing, and PISA analyses suggest that the functional oligomeric state of BT_3511 is probably a dimer (Figure 2).

    Figure 2.  Putative quaternary structure of BT_3511 (monomer A in green, monomer B in purple).

    GS13395A-dimer.png  

    The results of a DALI search are listed in Table 1.  Among the top results are protein kinases (e.g., PDB ids 2ux0, 2f86, 2w2c, and 1hkx) and type IV secretion system proteins (e.g., PDB ids 2bhm and 2cc3).  A superposition of BT_3511 with the top six DALI structural neighbors (Figure 3) reveals very similar overall topologies.

     

    Table 1.  Structural neighbors of BT_3511 as assessed by Dali.  Structures which have been superimposed with BT_3511 (see Figure 3) are color-highlighted.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2ux0 8.8 3.1 103 137 15 CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM
    2 2f86 8.6 3.1 100 129 6 HYPOTHETICAL PROTEIN K11E8.1D [Ref]
    3 2bhm 8.5 3.2 101 134 6 TYPE IV SECRETION SYSTEM PROTEIN VIRB8 [Ref]
    4 2w2c 8.4 2.9 99 131 13 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE
    5 2cc3 8.4 4.2 107 144 7 PROTEIN VIRB8 [Ref]
    6 1hkx 8.1 3.0 101 142 14 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE [Ref]
    7 3blz 8.0 3.1 91 123 3 NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION [TOPSAN]
    8 3fka 7.8 3.4 93 120 11 UNCHARACTERIZED NTF-2 LIKE PROTEIN [TOPSAN]
    9 3i0y 7.7 3.0 93 138 16 PUTATIVE POLYKETIDE CYCLASE [TOPSAN]
    10 3bb9 7.7 3.4 96 120 11 PUTATIVE ORPHAN PROTEIN

     

    Figure 3.  Superposition of BT_3511 (green) with top six DALI structural neighbors: 2ux0 (cyan), 2f86 (magenta), 2bhm (yellow), 2w2c (salmon), 2cc3 (gray), and 1hkx (purple).

    GS13395A-superpose-overall.png

    A PSI-BLAST search of BT_3511 yielded two hypothetical proteins: BACPLE_03306 from Bacteroides plebeius and CAPSP0001_2818 from Capnocytophaga sputigena.  A ConSurf analysis of the residue conservation among these proteins reveals a cleft in which several residues (i.e., Tyr-62, Asp-103, and Asp-111) are quite highly conserved; the electrostatic potential surface shows that this cleft is predominantly negatively-charged (Figures 4ab).

    Figure 4.  Molecular surface representations of BT_3511 mapping (a) residue conservation among BT_3511 and top two PSI-BLAST matches and (b) electrostatic potential.

    (a)                                                                        (b)

    GS13395A-consurf-labeled.png           GS13395A-emap-labeled.png

                              consurf_legend.png

     

    This cleft is located in a similar site to the binding pockets and/or active sites of other NTF2-like proteins [Ref].  Although the corresponding residues at this site among BT_3511 and the other NTF2-like proteins are not similar, the fact that the corresponding site in other NTF2-like proteins is known to be the active site and the fact that there are several conserved residues at this cleft in BT_3511 suggest that this site in BT_3511 may be functionally important and worth further biochemical investigation.
     

    Ligand Summary

    Reviews

    References

     

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