6E8D

Crystal structure of the Bacillus subtilis sliding clamp-MutL complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Binding of the regulatory domain of MutL to the sliding beta-clamp is species specific.

Almawi, A.W.Scotland, M.K.Randall, J.R.Liu, L.Martin, H.K.Sacre, L.Shen, Y.Pillon, M.C.Simmons, L.A.Sutton, M.D.Guarne, A.

(2019) Nucleic Acids Res. 47: 4831-4842

  • DOI: 10.1093/nar/gkz115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The β-clamp is a protein hub central to DNA replication and fork management. Proteins interacting with the β-clamp harbor a conserved clamp-binding motif that is often found in extended regions. Therefore, clamp interactions have -almost exclusively- ...

    The β-clamp is a protein hub central to DNA replication and fork management. Proteins interacting with the β-clamp harbor a conserved clamp-binding motif that is often found in extended regions. Therefore, clamp interactions have -almost exclusively- been studied using short peptides recapitulating the binding motif. This approach has revealed the molecular determinants that mediate the binding but cannot describe how proteins with clamp-binding motifs embedded in structured domains are recognized. The mismatch repair protein MutL has an internal clamp-binding motif, but its interaction with the β-clamp has different roles depending on the organism. In Bacillus subtilis, the interaction stimulates the endonuclease activity of MutL and it is critical for DNA mismatch repair. Conversely, disrupting the interaction between Escherichia coli MutL and the β-clamp only causes a mild mutator phenotype. Here, we determined the structures of the regulatory domains of E. coli and B. subtilis MutL bound to their respective β-clamps. The structures reveal different binding modes consistent with the binding to the β-clamp being a two-step process. Functional characterization indicates that, within the regulatory domain, only the clamp binding motif is required for the interaction between the two proteins. However, additional motifs beyond the regulatory domain may stabilize the interaction. We propose a model for the activation of the endonuclease activity of MutL in organisms lacking methyl-directed mismatch repair.


    Organizational Affiliation

    Genetics, Genomics and Bioinformatics Program, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Biochemistry, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Witebsky Center for Microbial Pathogenesis and Immunology, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Biochemistry, McGill University, Montreal, QC, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta sliding clamp,DNA mismatch repair protein MutL
A, B, C, D
512Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: dnaN (dnaG), mutL
Find proteins for P05649 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P05649
Find proteins for P49850 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P49850
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 59.020α = 80.30
b = 83.890β = 83.57
c = 128.260γ = 89.96
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-22
    Type: Data collection, Database references