2D6Y

Crystal Structure of transcriptional factor SCO4008 from Streptomyces coelicolor A3(2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

SCO4008, a Putative TetR Transcriptional Repressor from Streptomyces coelicolor A3(2), Regulates Transcription of sco4007 by Multidrug Recognition.

Hayashi, T.Tanaka, Y.Sakai, N.Okada, U.Yao, M.Watanabe, N.Tamura, T.Tanaka, I.

(2013) J Mol Biol 425: 3289-3300

  • DOI: 10.1016/j.jmb.2013.06.013
  • Primary Citation of Related Structures:  
    2D6Y

  • PubMed Abstract: 
  • SCO4008 from Streptomyces coelicolor A3(2) is a member of the TetR family. However, its precise function is not yet clear. In this study, the crystal structure of SCO4008 was determined at a resolution of 2.3Å, and its DNA-binding properties were analyzed ...

    SCO4008 from Streptomyces coelicolor A3(2) is a member of the TetR family. However, its precise function is not yet clear. In this study, the crystal structure of SCO4008 was determined at a resolution of 2.3Å, and its DNA-binding properties were analyzed. Crystal structure analysis showed that SCO4008 forms an Ω-shaped homodimer in which the monomer is composed of an N-terminal DNA-binding domain containing a helix-turn-helix and a C-terminal dimerization and regulatory domain possessing a ligand-binding cavity. The genomic systematic evolution of ligands by exponential enrichment and electrophoretic mobility shift assay revealed that four SCO4008 dimers bind to the two operator regions located between sco4008 and sco4007, a secondary transporter belonging to the major facilitator superfamily. Ligand screening analysis showed that SCO4008 recognizes a wide range of structurally dissimilar cationic and hydrophobic compounds. These results suggested that SCO4008 is a transcriptional repressor of sco4007 responsible for the multidrug resistance system in S. coelicolor A3(2).


    Organizational Affiliation

    Department of Food and Fermentation Science, Faculty of Food and Nutrition, Beppu University, Beppu, Oita 874-8501, Japan; Food Science and Nutrition, Graduate School of Food Science and Nutrition, Beppu University, Beppu, Oita 874-8501, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative tetR family regulatory proteinA, B202Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: SCO4008
UniProt
Find proteins for Q9ADP7 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9ADP7 
Go to UniProtKB:  Q9ADP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ADP7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.639α = 90
b = 47.334β = 90
c = 190.693γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2013-09-04
    Changes: Database references