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3npp

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

    Title Crystal structure of a Pfam DUF1093 family protein (BSU39620) from Bacillus subtilis at 2.15 A resolution. To be published
    Site JCSG
    PDB Id 3npp Target Id 416515
    Molecular Characteristics
    Source Bacillus subtilis subsp. subtilis str. 168
    Alias Ids TPS33791,NP_391841.1, 384449 Molecular Weight 9987.77 Da.
    Residues 86 Isoelectric Point 8.12
    Sequence rfnpfihqqdvyvqidrdgrhlspggteytldgynasgkkeevtffagkelrknaylkvkakgkyvetw eevkfedmpdsvqsklk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.15 Rfree 0.217
    Matthews' coefficent 3.54 Rfactor 0.179
    Waters 118 Solvent Content 65.22

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3npp
    1. Assessment of protein structure refinement in CASP9
    JL MacCallum, A Prez, MJ Schnieders - Proteins: Structure, , 2011 - Wiley Online Library
     
    2. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     

    Protein Summary

    Target BSU39620 (JCSG target accession code SP17552A, GenBank accession code NP_391841.1) is an 86-residue protein from Bacillus subtilis, a Gram-positive bacterium that is commonly found in soil.

    Target BSU39620 is currently annotated as hypothetical protein yxeA, a protein of unknown function but which is induced by the antibacterial protein LL-37 (probably via yxdJ) [Ref], [Ref].  The protein is  classified as belonging to Pfam PF06486, a family of proteins with an N-terminal signal sequence that are found exclusively in Gram-positive bacteria.  Currently there are over 600 members in this Pfam, of which this is the third structural representative.

    The structure of BSU39620 was solved by the Se-MAD method to a resolution of 2.15 Angstroms and reveals an alpha/beta fold whose core is similar to the OB-fold (oligonucleotide/oligosaccharide-binding fold).  This fold is ubiquitous in all three kingdoms and is often found in proteins which bind nucleic acids (e.g., tRNA synthetases, helicases, ligases, etc.  Refer to TOPSAN page for 3f1z for an example). 

    Both crystal packing and analytical size exclusion chromatography (anSEC) analyses suggest that BSU39620 is a monomer.

    Figure 1.  Structure of protein SMc02904  monomer: (a) gradiently colored from the N- (blue) to the C-terminus (red) and (b) colored according to secondary structure (beta-strands (red), helix (blue), loops (yellow)).

    (a)                                                                          (b)

    SP17552A-gradient.png        SP17552A-ss.png

     

    A structural neighbor search with DALI reveals the best matches to be the membrane associated protein BcR97A from Bacillus cereus (PDB id 2k5q) and the putative lipoprotein BcR103A, also from Bacillus cereus (PDB id 2k5w).  (Table 1).

    Table 1.  Top structural neighbors of BSU39620 as assessed by DALI.  Titles are highlighed in the same color as that of their corresponding structures in Figure 2.


    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2k5q 9.0 3.4 85 105 39 HYPOTHETICAL MEMBRANE ASSOCIATED PROTEIN BCR97A
    2 2k5w 8.2 2.9 75 111 31 HYPOTHETICAL CYTOSOLIC PROTEIN BCR103A
    3 1z9f 5.3 3.3 68 89 13 SINGLE-STRAND BINDING PROTEIN [Ref]
    4 3eiv 5.1 3.4 70 111 13 SINGLE-STRANDED DNA-BINDING PROTEIN 2 [Ref]

     

    Figure 2.  Superposition of BSU39620 (yellow) with top DALI structural neighbors 2k5q (blue), 2k5w (red), 1z9f (green), and 3eiv (purple).

    SP17552A-superpose.png

     

    Residue conservation analysis of BSU39620 and 10 sequence homologs which share ~30-40% sequence identity with BSU39620 reveal an area of high conservation which may be a binding site (Figure 3).

    Figure 3.  Residue conservation among BSU39620 and 10 sequence homologs which share ~30-40% sequence identity.  Residues that are highly conserved are in red and those not conserved are in blue.  Residues for which there is insufficient data to determine conservation level are in yellow (prepared with ConSurf).

    SP17552A-consurf.png

     

    Figure 4.  Electrostatic map of BSU39620.  Orientation is the same as in Figure 3.

    SP17552A-emap.png

    Ligand Summary

    Reviews

    References

     

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