Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80989.15 
• Atom Count: 5342 
• Residue Count: 720 
• Unique protein chains: 1

4P81

Structure of ancestral PyrR protein (AncORANGEPyrR)

• DOI: 10.2210/pdb4P81/pdb

• Classification: TRANSCRIPTION
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2014-03-29 Released: 2014-12-17 
• Deposition Author(s): Perica, T., Kondo, Y., Tiwari, S., McLaughlin, S., Steward, A., Reuter, N., Clarke, J., Teichmann, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.224 
• R-Value Work: 0.182 

Literature

Evolution of oligomeric state through allosteric pathways that mimic ligand binding.

Perica, T., Kondo, Y., Tiwari, S.P., McLaughlin, S.H., Kemplen, K.R., Zhang, X., Steward, A., Reuter, N., Clarke, J., Teichmann, S.A.

(2014) Science 346: 1254346-1254346

• PubMed: 25525255 
• DOI: 10.1126/science.1254346
• Primary Citation of Related Structures:  
  4P86, 4P84, 4P83, 4P82, 4P80, 4P3K


• PubMed Abstract: 
  

Evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. We showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. In this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the PyrR family of pyrimidine operon attenuators. In this family, a perfectly sequence-conserved helix that forms a tetrameric interface is exposed as solvent-accessible surface in dimeric orthologs. This means that mutations must be acting from a distance to destabilize the interface. We identified 11 key mutations controlling oligomeric state, all distant from the interfaces and outside ligand-binding pockets. Finally, we show that the key mutations introduce conformational changes equivalent to the conformational shift between the free versus nucleotide-bound conformations of the proteins.

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Organizational Affiliation: 

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Medical Research Council (MRC) Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ancestral PyrR protein (Orange)	A, B, C, D	180	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.224 
• R-Value Work: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 59.910	α = 90.00
b = 102.300	β = 90.00
c = 107.700	γ = 90.00

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-03-29 
• Released Date: 2014-12-17 
• Deposition Author(s): Perica, T., Kondo, Y., Tiwari, S., McLaughlin, S., Steward, A., Reuter, N., Clarke, J., Teichmann, S.A.

Revision History 

• Version 1.0: 2014-12-17
  Type: Initial release
• Version 1.1: 2014-12-24
  Type: Database references
• Version 1.2: 2014-12-31
  Type: Database references