2HO0

Structure of a Hyper-cleavable Monomeric Fragment of Phage Lambda Repressor Containing the Cleavage Site Region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Hyper-cleavable Monomeric Fragment of Phage lambda Repressor Containing the Cleavage Site Region.

Ndjonka, D.Bell, C.E.

(2006) J.Mol.Biol. 362: 479-489

  • DOI: 10.1016/j.jmb.2006.07.026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The key event in the switch from lysogenic to lytic growth of phage lambda is the self-cleavage of lambda repressor, which is induced by the formation of a RecA-ssDNA-ATP filament at a site of DNA damage. Lambda repressor cleaves itself at the peptid ...

    The key event in the switch from lysogenic to lytic growth of phage lambda is the self-cleavage of lambda repressor, which is induced by the formation of a RecA-ssDNA-ATP filament at a site of DNA damage. Lambda repressor cleaves itself at the peptide bond between Ala111 and Gly112, but only when bound as a monomer to the RecA-ssDNA-ATP filament. Here we have designed a hyper-cleavable fragment of lambda repressor containing the hinge and C-terminal domain (residues 101-229), in which the monomer-monomer interface is disrupted by two point mutations and a deletion of seven residues at the C terminus. This fragment crystallizes as a monomer and its structure has been determined to 1.8 A resolution. The hinge region, which bears the cleavage site, is folded over the active site of the C-terminal oligomerization domain (CTD) but with the cleavage site flipped out and exposed to solvent. Thus, the structure represents a non-cleavable conformation of the repressor, but one that is poised for cleavage after modest rearrangements that are presumably stabilized by binding to RecA. The structure provides a unique snapshot of lambda repressor in a conformation that sheds light on how its self-cleavage is tempered in the absence of RecA, as well as a framework for interpreting previous genetic and biochemical data concerning the RecA-mediated cleavage reaction.


    Organizational Affiliation

    Department of Molecular and Cellular Biochemistry, Ohio State University College of Medicine, Columbus, OH 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Repressor protein cI101-229DM-K192A
A
133Escherichia coliMutation(s): 2 
Gene Names: cI
Find proteins for Q7B004 (Escherichia coli)
Go to UniProtKB:  Q7B004
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.253 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 59.650α = 90.00
b = 59.650β = 90.00
c = 148.410γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata scaling
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance