6AMK | pdb_00006amk

Structure of Streptomyces venezuelae BldC-whiI opt complex

• PDB DOI: https://doi.org/10.2210/pdb6AMK/pdb
• NAKB: 6AMK

• Classification: dna binding protein/dna
• Organism(s): Streptomyces venezuelae, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 
  0.263 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

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

• PubMed: 29556010 
• 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.

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Organizational Affiliation: 
• Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA. [e-mail].
Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA. [e-mail].
Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.84 kDa 
• Atom Count: 1,698 
• Modeled Residue Count: 147 
• Deposited Residue Count: 188 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative DNA-binding protein	A, B	72	Streptomyces venezuelae	Mutation(s): 2  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 ID: 2
Molecule	Chains	Length	Organism	Image
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')	C [auth R]	22	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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')	D [auth Z]	22	synthetic construct

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free:  0.263 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.2	α = 90
b = 114.2	β = 90
c = 159	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data collection
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Data collection, Database references
• Version 1.2: 2018-11-07
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary