1PAR

DNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR CRYSTAL STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1PAR/pdb
• NAKB: 1PAR

• Classification: TRANSCRIPTION/DNA
• Organism(s): Lederbergvirus P22
• Mutation(s): No 


• Deposited: 1994-03-22 Released: 1994-07-31 
• Deposition Author(s): Raumann, B.E., Rould, M.A., Pabo, C.O., Sauer, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Observed: 0.225 

Literature

DNA recognition by beta-sheets in the Arc repressor-operator crystal structure.

Raumann, B.E., Rould, M.A., Pabo, C.O., Sauer, R.T.

(1994) Nature 367: 754-757

• PubMed: 8107872 
• DOI: https://doi.org/10.1038/367754a0
• Primary Citation of Related Structures:  
  1PAR


• PubMed Abstract: 
  

  Transcription of the ant gene during lytic growth of bacteriophage P22 (ref. 1) is regulated by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Here we report the co-crystal structure of this Arc tetramer-operator complex at 2.6 A resolution. As expected from genetic and structural studies and from the co-crystal structure of the homologous Escherichia coli MetJ repressor, each Arc dimer uses an antiparallel beta-sheet to recognize bases in the major groove. However, the Arc and MetJ complexes differ in several important ways: the beta-sheet-DNA interactions of Arc are far less symmetrical; DNA binding by Arc is accompanied by important conformational changes in the beta-sheet; and Arc uses a different part of its protein surface for dimer-dimer interactions.

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Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.45 kDa 
• Atom Count: 2,653 
• Modelled Residue Count: 252 
• Deposited Residue Count: 256 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ARC REPRESSOR)	C [auth A], D [auth B], E [auth C], F [auth D]	53	Lederbergvirus P22	Mutation(s): 0
UniProt
Find proteins for P03050 (Salmonella phage P22) Explore P03050  Go to UniProtKB:  P03050

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*T P*AP*TP*CP*AP*T)- 3')	A [auth E]	22	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*T P*AP*CP*TP*AP*T)- 3')	B [auth F]	22	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Observed: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.67	α = 90
b = 56.73	β = 106.9
c = 53.8	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-07-31 
Deposition Author(s): Raumann, B.E., Rould, M.A., Pabo, C.O., Sauer, R.T.

Revision History  

• Version 1.0: 1994-07-31
  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: 2024-02-14
  Changes: Data collection, Database references