6AMK

Structure of Streptomyces venezuelae BldC-whiI opt complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.288 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development.

Schumacher, M.A.den Hengst, C.D.Bush, M.J.Le, T.B.K.Tran, N.T.Chandra, G.Zeng, W.Travis, B.Brennan, R.G.Buttner, M.J.

(2018) Nat Commun 9: 1139-1139

  • DOI: 10.1038/s41467-018-03576-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Streptomycetes are notable for their complex life cycle and production of most clinically important antibiotics. A key factor that controls entry into development and the onset of antibiotic production is the 68-residue protein, BldC. BldC is a putat ...

    Streptomycetes are notable for their complex life cycle and production of most clinically important antibiotics. A key factor that controls entry into development and the onset of antibiotic production is the 68-residue protein, BldC. BldC is a putative DNA-binding protein related to MerR regulators, but lacks coiled-coil dimerization and effector-binding domains characteristic of classical MerR proteins. Hence, the molecular function of the protein has been unclear. Here we show that BldC is indeed a DNA-binding protein and controls a regulon that includes other key developmental regulators. Intriguingly, BldC DNA-binding sites vary significantly in length. Our BldC-DNA structures explain this DNA-binding capability by revealing that BldC utilizes a DNA-binding mode distinct from MerR and other known regulators, involving asymmetric head-to-tail oligomerization on DNA direct repeats that results in dramatic DNA distortion. Notably, BldC-like proteins radiate throughout eubacteria, establishing BldC as the founding member of a new structural family of regulators.


    Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA. maria.schumacher@duke.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative DNA-binding protein
A, B
72Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745)Mutation(s): 2 
Find proteins for F2REK9 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745))
Go to UniProtKB:  F2REK9
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*CP*AP*AP*TP*TP*CP*GP*GP*GP*TP*AP*AP*TP*TP*CP*GP*GP*GP*CP*A)-3')R22synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*TP*TP*AP*CP*CP*CP*GP*AP*AP*TP*TP*G)-3')Z22synthetic construct
Small Molecules
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: 3.288 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 114.200α = 90.00
b = 114.200β = 90.00
c = 159.000γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata collection
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-08-09 
  • Released Date: 2018-03-28 
  • Deposition Author(s): Schumacher, M.A.

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references