Solution structure of Escherichia coli UvrB C-terminal domain

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: MINIMAL ENERGY/VIOLATIONS 

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Solution Structure, Hydrodynamics and Thermodynamics of the Uvrb C-Terminal Domain.

Alexandrovich, A.A.Czisch, M.M.Frenkiel, T.T.Kelly, G.G.Goosen, N.N.Moolenaar, G.G.Chowdhry, B.B.Sanderson, M.M.Lane, A.A.

(2001) J Biomol Struct Dyn 19: 219-236

  • DOI: https://doi.org/10.1080/07391102.2001.10506734
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The solution structure, thermodynamic stability and hydrodynamic properties of the 55-residue C-terminal domain of UvrB that interacts with UvrC during excision repair in E. coli have been determined using a combination of high resolution NMR, ultracentrifugation, 15N NMR relaxation, gel permeation, NMR diffusion, circular dichroism and differential scanning calorimetry. The subunit molecular weight is 7,438 kDa., compared with 14.5+/-1.0 kDa. determined by equilibrium sedimentation, indicating a dimeric structure. The structure determined from NMR showed a stable dimer of anti-parallel helical hairpins that associate in an unusual manner, with a small and hydrophobic interface. The Stokes radius of the protein decreases from a high plateau value (ca. 22 A) at protein concentrations greater than 4 microM to about 18 A at concentrations less than 0.1 microM. The concentration and temperature-dependence of the far UV circular dichroism show that the protein is thermally stable (Tm ca. 71.5 degrees C at 36 microM). The simplest model consistent with these data was a dimer dissociating into folded monomers that then unfolds co-operatively. The van't Hoff enthalpy and dissociation constant for both transition was derived by fitting, with deltaH1=23 kJ mol(-1). K1(298)=0.4 microM and deltaH2= 184 kJ mol(-1). This is in good agreement with direct calorimetric analysis of the thermal unfolding of the protein, which gave a calorimetric enthalpy change of 181 kJ mol(-1) and a van't Hoff enthalpy change of 354 kJ mol(-1), confirming the dimer to monomer unfolding. The thermodynamic data can be reconciled with the observed mode of dimerisation. 15N NMR relaxation measurements at 14.1 T and 11.75 T confirmed that the protein behaves as an asymmetric dimer at mM concentrations, with a flexible N-terminal linker for attachment to the remainder of the UvrB protein. The role of dimerisation of this domain in the excision repair mechanism is discussed.

  • Organizational Affiliation

    Randall Centre for Molecular Mechanisms of Cell Function, New Hunt's House, King's College, London, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
63Escherichia coliMutation(s): 0 
Gene Names: UVRB
Find proteins for P0A8F8 (Escherichia coli (strain K12))
Explore P0A8F8 
Go to UniProtKB:  P0A8F8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8F8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: MINIMAL ENERGY/VIOLATIONS 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Database references
  • Version 1.4: 2020-01-15
    Changes: Other
  • Version 1.5: 2023-06-14
    Changes: Database references, Other
  • Version 1.6: 2024-06-19
    Changes: Data collection, Database references