PDBsum entry 6e8e

DNA binding protein

PDB id: 6e8e

Contents

Protein chains

468 a.a.

Ligands

GOL ×6

SO4 ×5

Waters ×191

PDB id:

6e8e

Name:

DNA binding protein

Title:

Crystal structure of the escherichia coli sliding clamp-mutl complex.

Structure:

Beta sliding clamp,DNA mismatch repair protein mutl. Chain: a. Synonym: sliding clamp,beta-clamp processivity factor,DNA polymerase iii beta sliding clamp subunit. Engineered: yes. Beta sliding clamp,DNA mismatch repair protein mutl. Chain: b. Synonym: sliding clamp,beta-clamp processivity factor,DNA polymerase iii beta sliding clamp subunit.

Source:

Escherichia coli (strain k12), escherichia coli o139:h28 (strain e24377a / etec). Organism_taxid: 83333, 331111. Strain: k12, e24377a / etec. Gene: dnan, b3701, jw3678, mutl, ece24377a_4728. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_taxid: 469008

Resolution:

2.25Å R-factor: 0.191 R-free: 0.225

Authors:

A.Guarne,A.W.Almawi

Key ref:

A.W.Almawi et al. (2019). Binding of the regulatory domain of MutL to the sliding β-clamp is species specific. Nucleic Acids Res, 47, 4831-4842. PubMed id: 30916336 DOI: 10.1093/nar/gkz115

Date:

28-Jul-18 Release date: 01-May-19

Protein chains

P0A988  (DPO3B_ECOLI) -  Beta sliding clamp from Escherichia coli (strain K12)

Seq: 366 a.a.

Struc: 468 a.a.

Protein chains

P23367  (MUTL_ECOLI) -  DNA mismatch repair protein MutL from Escherichia coli (strain K12)

Seq: 615 a.a.

Struc: 468 a.a.*

* PDB and UniProt seqs differ at 355 residue positions (black crosses)

DOI no: 10.1093/nar/gkz115

Nucleic Acids Res 47:4831-4842 (2019)

PubMed id: 30916336

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

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

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.