The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of predicted transcriptional regulator of TetR/AcrR family (YP_495839.1) from Novosphingobium aromaticivorans DSM 12444 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 2ras Target Id 376219
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS1669,YP_495839.1, 335915 Molecular Weight 23710.57 Da.
    Residues 211 Isoelectric Point 4.68
    Sequence massgtehdamrarlvdvaqaiveerggagltlselaaragisqanlsryfetredlmeaiadywfhpm veimedvlasdlpprrkmyeffarrfvvmrrkweadpvklqtyievgndyfeqvrsyidladhylgeii geamsdgafsglevdetislvnqmcapycalntmttfmerlsedklarivdavfdglsaqdrgarsltg lraa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.206
    Matthews' coefficent 2.64 Rfactor 0.177
    Waters 353 Solvent Content 53.38

    Ligand Information


    Google Scholar output for 2ras
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    2. Crystal structure of bovine lipoyltransferase in complex with lipoyl-AMP
    K Fujiwara, H Hosaka, M Matsuda - Journal of molecular , 2007 - Elsevier
    3. Crystal structure of a putative transcriptional regulator SCO0520 from Streptomyces coelicolorA3 (2) reveals an unusual dimer among TetR family proteins
    EV Filippova, M Chruszcz, M Cymborowski - Journal of structural and , 2011 - Springer

    Protein Summary

    Gene Saro_0558 from Novosphingobium aromaticivorans dsm 12444 encodes the YP_495839 protein, a predicted transcriptional regulator from the TetR/AcrR family (PF00440). Analysis of its genome context predicts a likely functional association (score 0.6) with its neighbor Saro_0559, a 5'-nucleotidase.

    Pre-SCOP classifies 2ras in the all alpha class, homeodomain-like superfamily, tetracyclin repressor-like N-terminal domain family. Similar to other members of this family, the 2ras structure can be divided into an N-terminal HTH fold, which likely binds DNA and a C-terminal regulatory domain. No biologically relevant ligand was found bound at the regulatory domain.  A search using DALI for structures similar to 2ras returns as top hits the transcriptional regulator PKSA-related PDB:2gfn (Z=14),  and several uncharacterized HTH transcriptional regulators (Z=13) like PDB:3crj, PDB:2dg8, PDB:1vi0.

    Another related TetR-like structure is the protein Saro_1072 from Novosphingobium aromaticivorans dsm 12444 determined by JCSG (2QTQ). There are significant conformational differences between the structures of 2RAS and 2QTQ.

    Ligand Summary





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