4H0E | pdb_00004h0e

Crystal Structure of mutant ORR3 in complex with NTD of AraR

• PDB DOI: https://doi.org/10.2210/pdb4H0E/pdb
• NAKB: 4H0E

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


• Deposited: 2012-09-08 Released: 2013-02-06 
• Deposition Author(s): Nair, D.T., Jain, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.253 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators.

Jain, D., Nair, D.T.

(2013) Nucleic Acids Res 41: 639-647

• PubMed: 23109551 
• DOI: https://doi.org/10.1093/nar/gks962
• Primary Citation Related Structures: 
  4EGY, 4EGZ, 4H0E


• PubMed Abstract: 
  

  Transcription factors modulate expression primarily through specific recognition of cognate sequences resident in the promoter region of target genes. AraR (Bacillus subtilis) is a repressor of genes involved in L-arabinose metabolism. It binds to eight different operators present in five different promoters with distinct affinities through a DNA binding domain at the N-terminus. The structures of AraR-NTD in complex with two distinct operators (ORA1 and ORR3) reveal that two monomers bind to one recognition motif (T/ANG) each in the bipartite operators. The structures show that the two recognition motifs are spaced apart by six bases in cases of ORA1 and eight bases in case of ORR3. This increase in the spacing in the operators by two base pairs results in a drastic change in the position and orientation of the second monomer on DNA in the case of ORR3 when compared with ORA1. Because AraR binds to the two operators with distinct affinities to achieve different levels of repression, this observation suggests that the variation in the spacing between core recognition motifs could be a strategy used by this transcription modulator to differentially influence gene expression.

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Organizational Affiliation: 
• Laboratory 4, National Centre for Biological Sciences, NCBS-TIFR, UAS-GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 32.96 kDa 
• Atom Count: 2,205 
• Modeled Residue Count: 193 
• Deposited Residue Count: 218 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arabinose metabolism transcriptional repressor	A, B	88	Bacillus subtilis	Mutation(s): 0  Gene Names: araC, araR, BSU33970, yvbS
UniProt
Find proteins for P96711 (Bacillus subtilis (strain 168)) Explore P96711  Go to UniProtKB:  P96711

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*CP*CP*GP*TP*AP*CP*AP*TP*TP*TP*TP*AP*T)-3'	C [auth U]	21	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*TP*AP*TP*AP*AP*AP*AP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*AP*AP*TP*T)-3'	D [auth T]	21	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth B], F [auth U], G [auth T]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	H [auth T]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.253 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.8	α = 90
b = 42.62	β = 114.92
c = 67.44	γ = 90

Software Package:

Software Name	Purpose
PXIII	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Nair, D.T., Jain, D.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description