Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.69 kDa 
• Atom Count: 1642 
• Residue Count: 166 
• Unique protein chains: 1

1A3C

PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, DIMERIC FORM

• DOI: 10.2210/pdb1A3C/pdb

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


• Deposited: 1998-01-20 Released: 1998-08-05 
• Deposition Author(s): Tomchick, D.R., Turner, R.J., Switzer, R.W., Smith, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.233 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Literature

Adaptation of an enzyme to regulatory function: structure of Bacillus subtilis PyrR, a pyr RNA-binding attenuation protein and uracil phosphoribosyltransferase.

Tomchick, D.R., Turner, R.J., Switzer, R.L., Smith, J.L.

(1998) Structure 6: 337-350

• PubMed: 9551555 
• DOI: 10.1016/s0969-2126(98)00036-7
• Primary Citation of Related Structures:  
  1A3C, 1A4X


• PubMed Abstract: 
  

The expression of pyrimidine nucleotide biosynthetic (pyr) genes in Bacillus subtilis is regulated by transcriptional attenuation. The PyrR attenuation protein binds to specific sites in pyr mRNA, allowing the formation of downstream terminator structures. UMP and 5-phosphoribosyl-1-pyrophosphate (PRPP), a nucleotide metabolite, are co-regulators with PyrR. The smallest RNA shown to bind tightly to PyrR is a 28-30 nucleotide stem-loop that contains a purine-rich bulge and a putative-GNRA tetraloop. PyrR is also a uracil phosphoribosyltransferase (UPRTase), although the relationship between enzymatic activity and RNA recognition is unclear, and the UPRTase activity of PyrR is not physiologically significant in B. subtilis. Elucidating the role of PyrR structural motifs in UMP-dependent RNA binding is an important step towards understanding the mechanism of pyr transcriptional attenuation.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRIMIDINE OPERON REGULATORY PROTEIN PYRR	A	181	Bacillus subtilis	Mutation(s): 0  Gene Names: pyrR EC: 2.4.2.9
Find proteins for P39765 (Bacillus subtilis (strain 168)) Explore P39765  Go to UniProtKB:  P39765

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SM	A	SAMARIUM (III) ION Sm DOSGOCSVHPUUIA-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.233 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.7	α = 90
b = 57.7	β = 129
c = 55	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

• Deposited Date: 1998-01-20 
• Released Date: 1998-08-05 
Deposition Author(s): Tomchick, D.R., Turner, R.J., Switzer, R.W., Smith, J.L.

Revision History 

• Version 1.0: 1998-08-05
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2018-03-21
  Changes: Advisory, Derived calculations, Other