1UMU

STRUCTURE DETERMINATION OF UMUD' BY MAD PHASING OF THE SELENOMETHIONYL PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the UmuD' protein and its regulation in response to DNA damage.

Peat, T.S.Frank, E.G.McDonald, J.P.Levine, A.S.Woodgate, R.Hendrickson, W.A.

(1996) Nature 380: 727-730

  • DOI: 10.1038/380727a0

  • PubMed Abstract: 
  • For life to be sustained, mistakes in DNA repair must be tolerated when damage obscures the genetic information. In bacteria such as Escherichia coli, DNA damage elicits the well regulated 'SOS response'. For the extreme case of damage that cannot be ...

    For life to be sustained, mistakes in DNA repair must be tolerated when damage obscures the genetic information. In bacteria such as Escherichia coli, DNA damage elicits the well regulated 'SOS response'. For the extreme case of damage that cannot be repaired by conventional enzymes, there are proteins that allow the replication of DNA through such lesions, but with a reduction in the fidelity of replication. Essential proteins in this mutagenic process are RecA, DNA polymerase III, UmuD, UmuD' and UmuC (umu: UV mutagenesis). Regulation of this response involves a RecA-mediated self-cleavage of UmuD to produce UmuD'. To understand this system in more detail, we have determined the crystal structure of the E. coli UmuD' mutagenesis protein at 2.5 A resolution. Globular heads folded in an unusual Beta-structure associate to form molecular dimers, and extended amino-terminal tails associate to produce crystallized filaments. The structure provides insight into the mechanism of the self-cleavage reaction that UmuD-like proteins undergo as part of the global SOS response.


    Related Citations: 
    • Production and Crystallization of a Selenomethionyl Variant of UmuD', an Escherichia Coli SOS Response Protein
      Peat, T.S.,Frank, E.G.,Woodgate, R.,Hendrickson, W.A.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Deparment of Biochemistry and Molecular Biophysics, Columbia University, NY 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UMUD'
A, B
116Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: umuD
EC: 3.4.21.-
Find proteins for P0AG11 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG11
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 52.800α = 90.00
b = 52.800β = 90.00
c = 160.100γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
MADSYSphasing
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance