Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.86 kDa 
• Atom Count: 1636 
• Residue Count: 211 
• Unique protein chains: 1

1UMU

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

• DOI: 10.2210/pdb1UMU/pdb

• Classification: SOS MUTAGENESIS
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-03-07 Released: 1996-08-01 
• Deposition Author(s): Peat, T.S., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.303 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

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

• PubMed: 8614470 
• DOI: 10.1038/380727a0
• Primary Citation of Related Structures:  
  1UMU


• 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 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.

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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 --: --

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UMUD'	A, B	116	Escherichia coli	Mutation(s): 0  EC: 3.4.21
Find proteins for P0AG11 (Escherichia coli (strain K12)) Explore P0AG11  Go to UniProtKB:  P0AG11

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.303 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.8	α = 90
b = 52.8	β = 90
c = 160.1	γ = 90

Software Package:

Software Name	Purpose
MADSYS	phasing
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-03-07 
• Released Date: 1996-08-01 
Deposition Author(s): Peat, T.S., Hendrickson, W.A.

Revision History 

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