1AY9

WILD-TYPE UMUD' FROM E. COLI

• PDB DOI:  https://doi.org/10.2210/pdb1AY9/pdb

• Classification: MUTAGENESIS PROTEIN
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1997-11-15 Released: 1998-01-28 
• Deposition Author(s): Peat, T.S., Frank, E.G., Mcdonald, J.P., Levine, A.S., Woodgate, R., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.287 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

The UmuD' protein filament and its potential role in damage induced mutagenesis.

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

(1996) Structure 4: 1401-1412

• PubMed: 8994967 
• DOI: https://doi.org/10.1016/s0969-2126(96)00148-7
• Primary Citation of Related Structures:  
  1AY9


• PubMed Abstract: 
  

Damage induced 'SOS mutagenesis' may occur transiently as part of the global SOS response to DNA damage in bacteria. A key participant in this process is the UmuD protein, which is produced in an inactive from but converted to the active form, UmuD', by a RecA-mediated self-cleavage reaction. UmuD', together with UmuC and activated RecA (RecA*), enables the DNA polymerase III holoenzyme to replicate across chemical and UV induced lesions. The efficiency of this reaction depends on several intricate protein-protein interactions.

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Related Citations: 

• 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

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.33 kDa 
• Atom Count: 1,628 
• Modelled Residue Count: 216 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UMUD PROTEIN	A, B	108	Escherichia coli	Mutation(s): 0  EC: 3.4.21
UniProt
Find proteins for P0AG11 (Escherichia coli (strain K12)) Explore P0AG11  Go to UniProtKB:  P0AG11

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.287 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.1	α = 90
b = 53.1	β = 90
c = 164.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Peat, T.S., Frank, E.G., Mcdonald, J.P., Levine, A.S., Woodgate, R., Hendrickson, W.A.

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Other, Refinement description