1LQ1

DNA Complexed Structure of the Key Transcription Factor Initiating Development in Sporulation Bacteria

• PDB DOI: https://doi.org/10.2210/pdb1LQ1/pdb
• NAKB: 1LQ1

• Classification: TRANSCRIPTION/DNA
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-05-08 Released: 2002-08-23 
• Deposition Author(s): Zhao, H., Msadek, T., Zapf, J., Madhusudan, Hoch, J.A., Varughese, K.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 

Literature

DNA complexed structure of the key transcription factor initiating development in sporulating bacteria.

Zhao, H., Msadek, T., Zapf, J., Madhusudan, Hoch, J.A., Varughese, K.I.

(2002) Structure 10: 1041-1050

• PubMed: 12176382 
• DOI: https://doi.org/10.1016/s0969-2126(02)00803-1
• Primary Citation of Related Structures:  
  1LQ1


• PubMed Abstract: 
  

  Sporulation in Bacillus species, the ultimate bacterial adaptive response, requires the precisely coordinated expression of a complex genetic pathway, and is initiated through the accumulation of the phosphorylated form of Spo0A, a pleiotropic response regulator transcription factor. Spo0A controls the transcription of several hundred genes in all spore-forming Bacilli including genes for sporulation and toxin regulation in pathogens such as Bacillus anthracis. The crystal structure of the effector domain of Spo0A from Bacillus subtilis in complex with its DNA target was determined. In the crystal lattice, two molecules form a tandem dimer upon binding to adjacent sites on DNA. The protein:protein and protein:DNA interfaces revealed in the crystal provide a basis for interpreting the transcription activation process and for the design of drugs to counter infections by these bacteria.

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Organizational Affiliation: 

Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 73.18 kDa 
• Atom Count: 4,909 
• Modelled Residue Count: 493 
• Deposited Residue Count: 544 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stage 0 sporulation protein A	E [auth A], F [auth B], G [auth C], H [auth D]	120	Bacillus subtilis	Mutation(s): 0  Gene Names: SPO0A
UniProt
Find proteins for P06534 (Bacillus subtilis (strain 168)) Explore P06534  Go to UniProtKB:  P06534

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3'	A [auth E], C [auth G]	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*AP*AP*AP*AP*TP*TP*CP*GP*AP*CP*AP*CP*GP*A)-3'	B [auth F], D [auth H]	16	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.917	α = 90
b = 83.301	β = 94.18
c = 91.241	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-23 
Deposition Author(s): Zhao, H., Msadek, T., Zapf, J., Madhusudan, Hoch, J.A., Varughese, K.I.

Revision History  

• Version 1.0: 2002-08-23
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references