2ARC | pdb_00002arc

ESCHERICHIA COLI REGULATORY PROTEIN ARAC COMPLEXED WITH L-ARABINOSE

• PDB DOI: https://doi.org/10.2210/pdb2ARC/pdb

• Classification: TRANSCRIPTION FACTOR
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-10-29 Released: 1997-05-15 
• Deposition Author(s): Soisson, S.M., Wolberger, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Structural basis for ligand-regulated oligomerization of AraC.

Soisson, S.M., MacDougall-Shackleton, B., Schleif, R., Wolberger, C.

(1997) Science 276: 421-425

• PubMed: 9103202 
• DOI: https://doi.org/10.1126/science.276.5311.421
• Primary Citation Related Structures: 
  2ARA, 2ARC


• PubMed Abstract: 
  

  The crystal structure of the arabinose-binding and dimerization domain of the Escherchia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The 1.5 angstrom structure of the arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the 2.8 angstrom structure of the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface. The ligand-gated oligomerization as seen in AraC provides the basis of a plausible mechanism for modulating the protein's DNA-looping properties.

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Organizational Affiliation: 
• Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.44 kDa 
• Atom Count: 3,124 
• Modeled Residue Count: 325 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARABINOSE OPERON REGULATORY PROTEIN	A, B	164	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A9E0 (Escherichia coli (strain K12)) Explore P0A9E0  Go to UniProtKB:  P0A9E0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARA	C [auth A], D [auth B]	alpha-L-arabinopyranose C5 H10 O5 SRBFZHDQGSBBOR-QMKXCQHVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.75	α = 90
b = 93.84	β = 95.62
c = 50.33	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-05-15 
Deposition Author(s): Soisson, S.M., Wolberger, C.

Revision History  

• Version 1.0: 1997-05-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Structure summary