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

    Title Crystal structure of STRUCTURAL GENOMICS, UNKNOWN FUNCTION (YP_928783.1) from SHEWANELLA AMAZONENSIS SB2B at 2.50 A resolution. To be published
    Site JCSG
    PDB Id 3ke2 Target Id 400661
    Molecular Characteristics
    Source Shewanella amazonensis sb2b
    Alias Ids TPS28022,YP_928783.1, 325656 Molecular Weight 12755.56 Da.
    Residues 116 Isoelectric Point 5.63
    Sequence mtqdnasgdqvskqhkaflrklylahlmddarhnllslgkltgmprrtlqdaiasfadigievefvqdg erhnagyyrirtwgpissawmdthvdevksllgvddadgqatagnga
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.50 Rfree 0.254
    Matthews' coefficent 2.45 Rfactor 0.214
    Waters 60 Solvent Content 49.87

    Ligand Information


    Google Scholar output for 3ke2

    Protein Summary

    Gene Sama_2911 from Shewanella amazonensis sb2b encodes the YP_928783 protein that belongs to the DUF2131 Pfam A class (an uncharacterized protein group conserved only in bacteria with two highly conserved Trp residues towards the C-terminus).

    The structure, 3ke2, was determined from a genetic construct in which Asp 107 is replaced with a Val residue. It was determined at a resolution of 2.5 Angstroms using two-wavelength Se-Multiwavelength Anomalous diffraction methods for phasing.


    Shown above is a rainbow colored ribbon representation of the 3ke2 structure with the N-terminal region in blue and the C-terminal region in red. A search of the SCOP database shows that 3ke2 most likely belongs to the "Winged helix" DNA Binding Domain SCOP Superfamily, Lrp/AsnC-like transcriptional regulator N-terminal domain family. The crystal structure and analytical size exclusion chromatography suggest that the dimer is a significant oligomerization state.


    Shown above is a ribbon representation of the dimer with the individual monomers colored in yellow and blue. A DALI structural similarity search shows that the 3ke2 structure is similar to those shown in the table below.


    PDB ID Z-score rmsd (Ang) lalign nresi %seq ID Description
    2h09 8.1 3.2 83 127 10 Diptheria Toxin Repressor-Like Protein from E. Coli.
    3bdd 7.2 2.8 78 140 6 Putative Multiple Antibiotic Resistance Repressor (MarR) from Streptococcus suis 89/1591
    2hzt 7.2 4.7 88  98 10 HTH-type Transcriptional Regulator ytcD
    2hr3 7.1 3.3 75 140 8 Putative Transcriptional Regulator from Psuedomonas aeruginosa
    3f8f 7.1 3.6 84 114 12 Multidrug Binding Transcriptional Regulator LmrR Complexed with Daunomycin
    3bj6 7.0 3.0 80 152 10  MarR Family Transcriptional Regulator SP03579
    1j5y 7.0 2.7 70 172 10 Transcriptional Regulator TM1602 from Thermotoga maritima.
    1r1t 7.0 2.6 70 99 14  Cyanobacterial Metallothionein Repressor SmtB in the apo-form.
    3f8c 7.0 3.2 82 103 15 Multidrug Binding Tracsciprional Regulator LmrR Complexed with Hoescht 33342
    3f3x 7.0 3.5 87 139 7 Transcriptional Regulator BldR from Sulfobus Solfataricus


     Other servers provide also matches, although weak and without overlap, to the family of HTH-type of transcription factors:

    -HHpred: 3cuo (P-val=1.2e-5); 1sfx (1.9e-5); 1u2w (2.1e-5)

    -SSM: 2p5l (SSE=43%); 1bby (43%); 3f21 (71%); 2zkz (71%)

    -FATCAT: 1j5y (P-val=5.3e-8); 1bia (2.5e-6)


    Pfam Summary: The results form the EBI-structure-comparison tool suggest that YP_928783 is a winged helix DNA-binding protein. The sequence is similar to the DUF2131 group, and so I have added a sentence at the bottom of the annotation to suggest that it is probably a DNA-binging domain, and I have added it to the clan HTH (CL0123), a very large clan.

    Ligand Summary




    No references found.

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