Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43400.04 
• Atom Count: 3005 
• Residue Count: 357 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2PUE

CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES

• DOI: 10.2210/pdb2PUE/pdb
• NDB: PDR043

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli BL21
• Mutation(s): 1 


• Deposited: 1997-10-04 Released: 1998-05-06 
• Deposition Author(s): Lu, F., Schumacher, M.A., Arvidson, D.N., Haldimann, A., Wanner, B.L., Zalkin, H., Brennan, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å

Literature

Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190.

Lu, F., Schumacher, M.A., Arvidson, D.N., Haldimann, A., Wanner, B.L., Zalkin, H., Brennan, R.G.

(1998) Biochemistry 37: 971-982

• PubMed: 9454587 
• DOI: 10.1021/bi971942s
• Primary Citation of Related Structures:  
  2PUG, 2PUF


• PubMed Abstract: 
  

Guanine or hypoxanthine, physiological corepressors of the Escherichia coli purine repressor (PurR), promote formation of the ternary PurR-corepressor-operator DNA complex that functions to repress pur operon gene expression. Structure-based predictions on the importance of Arg190 in determining 6-oxopurine specificity and corepressor binding affinity were tested by mutagenesis, analysis of in vivo function, and in vitro corepressor binding measurements. Replacements of Arg190 with Ala or Gln resulted in functional repressors in which binding of guanine and hypoxanthine was retained but specificity was relaxed to permit binding of adenine. X-ray structures were determined for ternary complexes of mutant repressors with purines (adenine, guanine, hypoxanthine, and 6-methylpurine) and operator DNA. These structures indicate that R190A binds guanine, hypoxanthine, and adenine with nearly equal, albeit reduced, affinity in large part because of a newly made compensatory hydrogen bond between the rotated hydroxyl side chain of Ser124 and the exocyclic 6 positions of the purines. Through direct and water-mediated contacts, the R190Q protein binds adenine with a nearly 75-fold higher affinity than the wild type repressor while maintaining wild type affinity for guanine and hypoxanthine. The results establish at the atomic level the basis for the critical role of Arg190 in the recognition of the exocyclic 6 position of its purine corepressors and the successful redesign of corepressor specificity.

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Related Citations: 

• Crystal Structure of LacI Member, PurR, Bound to DNA: Minor Groove Binding by Alpha Helices
  Schumacher, M.A.,Choi, K.Y.,Zalkin, H.,Brennan, R.G.
  (1994) Science 266: 763




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Organizational Affiliation: 

Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-1153, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (PURINE REPRESSOR )	A	340	Escherichia coli (strain K12)	Mutation(s): 1  Gene Names: purR
Find proteins for P0ACP7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ACP7

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')	B	17	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ADE	A	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DNA	Kd: 33000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 175.810	α = 90.00
b = 95.170	β = 90.00
c = 81.310	γ = 90.00

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-10-04 
• Released Date: 1998-05-06 
• Deposition Author(s): Lu, F., Schumacher, M.A., Arvidson, D.N., Haldimann, A., Wanner, B.L., Zalkin, H., Brennan, R.G.

Revision History 

• Version 1.0: 1998-05-06
  Type: Initial release
• Version 1.1: 2008-05-22
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-04-04
  Type: Data collection