6e8e

From Proteopedia

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

Structural highlights

6e8e is a 2 chain structure with sequence from Escherichia coli K-12 and Escherichia coli O139:H28 str. E24377A. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.25Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO3B_ECOLI DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.MUTL_ECOLI This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a "molecular matchmaker", a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of the final effector complex. The ATPase activity of MutL is stimulated by DNA.

Publication Abstract from PubMed

The beta-clamp is a protein hub central to DNA replication and fork management. Proteins interacting with the beta-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 beta-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 beta-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 beta-clamps. The structures reveal different binding modes consistent with the binding to the beta-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.

Binding of the regulatory domain of MutL to the sliding beta-clamp is species specific.,Almawi AW, Scotland MK, Randall JR, Liu L, Martin HK, Sacre L, Shen Y, Pillon MC, Simmons LA, Sutton MD, Guarne A Nucleic Acids Res. 2019 Mar 27. pii: 5420525. doi: 10.1093/nar/gkz115. PMID:30916336^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Almawi AW, Scotland MK, Randall JR, Liu L, Martin HK, Sacre L, Shen Y, Pillon MC, Simmons LA, Sutton MD, Guarne A. Binding of the regulatory domain of MutL to the sliding beta-clamp is species specific. Nucleic Acids Res. 2019 Mar 27. pii: 5420525. doi: 10.1093/nar/gkz115. PMID:30916336 doi:http://dx.doi.org/10.1093/nar/gkz115