Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 104850.02 
• Atom Count: 6640 
• Residue Count: 872 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

4GCK

structure of no-dna complex

• DOI: 10.2210/pdb4GCK/pdb
• NDB: NA1964

• Classification: dna binding protein/DNA
• Organism(s): Klebsiella pneumoniae (strain 342)
• Expression System: Escherichia coli


• Deposited: 2012-07-30 Released: 2013-06-19 
• Deposition Author(s): Schumacher, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.243 
• R-Value Work: 0.218 

Literature

SlmA forms a higher-order structure on DNA that inhibits cytokinetic Z-ring formation over the nucleoid.

Tonthat, N.K., Milam, S.L., Chinnam, N., Whitfill, T., Margolin, W., Schumacher, M.A.

(2013) Proc.Natl.Acad.Sci.USA 110: 10586-10591

• PubMed: 23754405 
• DOI: 10.1073/pnas.1221036110
• Primary Citation of Related Structures:  
  4GFL, 4GFK, 4GCT, 4GCL


• PubMed Abstract: 
  

The spatial and temporal control of Filamenting temperature sensitive mutant Z (FtsZ) Z-ring formation is crucial for proper cell division in bacteria. In Escherichia coli, the synthetic lethal with a defective Min system (SlmA) protein helps mediate nucleoid occlusion, which prevents chromosome fragmentation by binding FtsZ and inhibiting Z-ring formation over the nucleoid. However, to perform its function, SlmA must be bound to the nucleoid. To deduce the basis for this chromosomal requirement, we performed biochemical, cellular, and structural studies. Strikingly, structures show that SlmA dramatically distorts DNA, allowing it to bind as an orientated dimer-of-dimers. Biochemical data indicate that SlmA dimer-of-dimers can spread along the DNA. Combined structural and biochemical data suggest that this DNA-activated SlmA oligomerization would prevent FtsZ protofilament propagation and bundling. Bioinformatic analyses localize SlmA DNA sites near membrane-tethered chromosomal regions, and cellular studies show that SlmA inhibits FtsZ reservoirs from forming membrane-tethered Z rings. Thus, our combined data indicate that SlmA DNA helps block Z-ring formation over chromosomal DNA by forming higher-order protein-nucleic acid complexes that disable FtsZ filaments from coalescing into proper structures needed for Z-ring creation.

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Organizational Affiliation: 

Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Nucleoid occlusion factor SlmA	A, B, C, D	212	Klebsiella pneumoniae (strain 342)	Mutation(s): 0  Gene Names: slmA
Find proteins for B5XTG2 (Klebsiella pneumoniae (strain 342)) Go to UniProtKB:  B5XTG2

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')	W,Z	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.243 
• R-Value Work: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 71.490	α = 90.00
b = 80.750	β = 90.00
c = 201.300	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
MOLREP	phasing
ADSC	data collection
SCALA	data scaling
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-30 
• Released Date: 2013-06-19 
• Deposition Author(s): Schumacher, M.A.

Revision History 

• Version 1.0: 2013-06-19
  Type: Initial release
• Version 1.1: 2013-07-10
  Type: Database references