2PUB | pdb_00002pub

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

• PDB DOI: https://doi.org/10.2210/pdb2PUB/pdb
• NAKB: 2PUB

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 1997-10-04 Released: 1998-05-06 
• Deposition Author(s): Schumacher, R.G., Choi, K.Y., Zalkin, H., Brennan, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Work: 
  0.171 (Depositor) 

Literature

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: 763-770

• PubMed: 7973627 
• DOI: https://doi.org/10.1126/science.7973627
• Primary Citation Related Structures: 
  1PNR, 2PUA, 2PUB, 2PUC, 2PUD


• PubMed Abstract: 
  

  The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54', into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland 97201-3098.

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: 43.34 kDa 
• Atom Count: 3,054 
• Modeled Residue Count: 355 
• Deposited Residue Count: 357 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PURINE REPRESSOR	B [auth A]	340	Escherichia coli	Mutation(s): 1  Gene Names: PURR
UniProt
Find proteins for P0ACP7 (Escherichia coli (strain K12)) Explore P0ACP7  Go to UniProtKB:  P0ACP7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')	A [auth B]	17	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	C [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Work:  0.171 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.81	α = 90
b = 94.87	β = 90
c = 81.75	γ = 90

Software Package:

Software Name	Purpose
DIFFERENCE	model building
TNT	refinement
ADSC	data collection
DIFFERENCE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-06 
Deposition Author(s): Schumacher, R.G., Choi, K.Y., Zalkin, H., Brennan, M.A.

Revision History  

• Version 1.0: 1998-05-06
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-03-08
  Changes: Structure summary
• Version 1.4: 2018-04-04
  Changes: Data collection
• Version 1.5: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.6: 2024-02-21
  Changes: Data collection