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

Experimental Data Snapshot

  • Resolution: 2.34 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1093/nar/gkz115
  • Primary Citation of Related Structures:  
    6E8D, 6E8E

  • 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- 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta sliding clamp,DNA mismatch repair protein MutL
A, B, C, D
512Bacillus subtilisMutation(s): 0 
Gene Names: B4417_2457mutLB4417_3449
Find proteins for P49850 (Bacillus subtilis (strain 168))
Explore P49850 
Go to UniProtKB:  P49850
Find proteins for P05649 (Bacillus subtilis (strain 168))
Explore P05649 
Go to UniProtKB:  P05649
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP49850P05649
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.34 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.02α = 80.3
b = 83.89β = 83.57
c = 128.26γ = 89.96
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2020-10-07
    Changes: Derived calculations