6E8E

Crystal structure of the Escherichia coli sliding clamp-MutL complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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
  • Structures With Same Primary Citation

  • 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

    Department of Biochemistry, McGill University, Montreal, QC, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta sliding clamp,DNA mismatch repair protein MutL
A
517Escherichia coli K-12Escherichia coli O139:H28 str. E24377A
This entity is chimeric
Mutation(s): 0 
Gene Names: dnaNb3701JW3678
Find proteins for P0A988 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A988
Find proteins for P23367 (Escherichia coli (strain K12))
Go to UniProtKB:  P23367
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta sliding clamp,DNA mismatch repair protein MutL
B
517Escherichia coli K-12Escherichia coli O139:H28 str. E24377A
This entity is chimeric
Mutation(s): 0 
Gene Names: dnaNb3701JW3678
Find proteins for P0A988 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A988
Find proteins for P23367 (Escherichia coli (strain K12))
Go to UniProtKB:  P23367
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.39α = 90
b = 103.21β = 90
c = 141.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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