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 6AMA | pdb_00006ama

Structure of S. coelicolor/S. venezuelae BldC-smeA-ssfA complex to 3.09 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 
    0.281 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6AMA

This is version 1.2 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: https://doi.org/10.1038/s41467-018-03576-3
  • Primary Citation Related Structures: 
    6AMA, 6AMK

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 147.33 kDa 
  • Atom Count: 8,733 
  • Modeled Residue Count: 800 
  • Deposited Residue Count: 979 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative DNA-binding protein71Streptomyces venezuelaeMutation(s): 0 
Gene Names: AQF52_4259
UniProt
Find proteins for F2REK9 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745))
Explore F2REK9 
Go to UniProtKB:  F2REK9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2REK9
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (99-MER)L [auth N]99synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (99-MER)M [auth R]99synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free:  0.281 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.351α = 90
b = 159.351β = 90
c = 130.829γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description