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3nrg

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

    Title Crystal structure of a TetR family transcriptional regulator (Caur_2714) from CHLOROFLEXUS AURANTIACUS J-10-FL at 2.56 A resolution. To be published
    Site JCSG
    PDB Id 3nrg Target Id 399092
    Molecular Characteristics
    Source Chloroflexus aurantiacus j-10-fl
    Alias Ids TPS29686,YP_001636308.1, _0114.002261_, _0073.002805_, 327910 Molecular Weight 24781.13 Da.
    Residues 216 Isoelectric Point 5.16
    Sequence mptetffnlpeekrsrlidvlldefaqndydsvsinriteragiakgsfyqyfadkkdcylyliqlgie qktaflrqtppasttdmfaylrwlldvgiqfqfhnprlaqiaykalyddvplpaetmqvirhgsfayfk qlveqgiadgslvpdldadtaafvlnvvftelgnhlierfavnpaellreggivllqpamrrvieqvid ilergmrrr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 5
    Resolution (Å) 2.56 Rfree 0.243
    Matthews' coefficent 2.39 Rfactor 0.207
    Waters 122 Solvent Content 48.61

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3nrg
    1. 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
     
    2. A simple and efficient statistical potential for scoring ensembles of protein structures
    P Cossio, D Granata, A Laio, F Seno, A Trovato - Scientific Reports, 2012 - nature.com
     
    3. Structural basis for the transcriptional regulation of heme homeostasis in Lactococcus lactis
    H Sawai, M Yamanaka, H Sugimoto, Y Shiro - Journal of Biological , 2012 - ASBMB
     

    Protein Summary

    Update from Pfam I have searched this and found it to carry a: TetR_N (PF00440) domain, Bacterial regulatory proteins, tetR family. It appears to be a DNA-binding domain. There are several structures for this family.:

    The amino acid sequence of target id 399092 shows similarity to members of the TetR_N (PF00440) Pfam class with 344 structures for this Pfam class deposited in the PDB. The structure of target ID has been determined at a resolution of 2.56 Angstroms using two-wavelength Se-MAD phasing. Shown below is a ribbons representation of the monomeric structure of target ID with the colors blended along the polypeptide chain. The N-terminal end is in blue and the C-terminal end is in red.

    MI9424B_monomer.png

     

    Analytical size exclusion chromatography with static light scattering indicates that the monomer is a significant oligomerization state. In addition crystal packing suggests that a dimer is a significant oligomerization state. Shown below is a ribbons representation of the dimer with the two subunits in blue and yellow respectively.

     

    dimer.png

     

     

     

     

     

     

     

     

     

     

     

     The crystal shows five monomers in the crystallographic asymmetric unit. Comparison of the five monomers shows some structural changes occur in three connecting surface loops between residues 72-84, 142-148, and 180-196.

     

    overlap2.bmp

     

     Based on sequence and structural similarity, target ID 399092 likely functions as a transcriptional repressor and belongs to the DNA/RNA binding 3-helical bundle SCOP fold. A DALI structural comparison seach shows that the structure of target ID 399092 is similar to the following structures:

     

    PDB ID Z-score rmsd lalign number residues % sequence id Description
    2id6 14.6 3.5 194 202 15 Transcriptional regulator (TM1030) at 1.75 A resolution.
    3f1b 14.5 3.0 177 183 16 TetR-like transcriptional regulator from Rhodococcus sp. RHA1.
    1z77 14.3 3.6 194 200 16 Transcriptional regulator TM1030 from Thermotoga maritima solved by an unusual MAD experiment.
    3dew 14.2 2.9 182 192 23 putative TetR family transcriptional regulator from Geobacter sulfurreducens PCA
    3kz9 14.2 3.6 186 201 12 Master transcriptional regulator, SmcR, in Vibrio vulnificus provides insight into its DNA recognition mechanism. 
    1jt0 14.2 3.3 178 188 10  Cooperative QacR-DNA complex
    1jum 13.9 3.2 178 186 10  Multidrug binding transcriptional repressor QacR bound to the natural drug berberine.
    1qvu 13.8 3.2  177  186 10  Multidrug binding transcriptional repressor QaCE bound to two drugs: ethidium and proflavine.
     2hq5 13.8 3.2 176 185 11  Multidrug binding protein QacR from Staphylococcus aureus co-crystallized with compound DB359
    1rpw 13.8 3.3 178 186 11 The multidrug binding protein Qacr Bound to the diamide hexamidine.
    2pbx 13.6 3.3  181 196 14  Vibrio cholerae HapR
    1t56 13.6 4.0 186 193 17 TetR/CamR family repressor Mycobacterium tuberculosis EthR implicated in ethionamide resistance

    Ligand Summary

    Reviews

    References

     

    No references found.

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