8XLA

Mismatch Repair Complex

Summary for 8XLA

• Entry DOI: 10.2210/pdb8xla/pdb
• Descriptor: Beta sliding clamp, DNA mismatch repair protein MutL (2 entities in total)
• Functional Keywords: dna mismatch repair, endonuclease, processivity clamp, dna binding protein
• Biological source: Neisseria gonorrhoeae FA 1090; More
• Total number of polymer chains: 7
• Total formula weight: 244254.11

Authors

Nirwal, S.,Nair, D.T. (deposition date: 2023-12-25, release date: 2025-04-16)

Primary citation

Nirwal, S.,Jha, R.,Narayanan, N.,Sharma, M.,Kulkarni, D.S.,Sharma, D.,Babu, A.S.,Suthar, D.K.,Rao, D.N.,Nair, D.T.
The structure of the MutL-CTD:processivity-clamp complex provides insight regarding strand discrimination in non-methyl-directed DNA mismatch repair.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Many prokaryotes, including members of the Neisseria species, lack MutH and cannot employ methyl-directed DNA mismatch repair (MMR). The nick on the daughter strand is created by the endonuclease activity present in the C-terminal domain (CTD) of the MutL homodimer. MutL-CTD is known to interact with the processivity-clamp. The crystal structure of the homodimeric MutL-CTD from Neisseria (NgoL-CTD) in complex with homodimeric processivity-clamp (Nβ-Clamp) shows that each NgoL-CTD monomer binds to a Nβ-Clamp monomer through the conserved motif III (517QHLLIP522). The structure and allied biochemical studies plus in vivo growth assays conducted with wild-type (wt) plus mutant proteins shows that the endonuclease dimer sits transversely across the C-terminal face of the Nβ-Clamp ring. The comparison of the structure with that of the partial prokaryotic replisome suggests that the relative orientation of DNA, Nβ-Clamp, and NgoL-CTD may direct the daughter strand towards one of the active sites in endonuclease homodimer. Nicking assays conducted with wt and mutant NgoL-CTD in the presence and absence of Nβ-Clamp support this inference. Overall, our studies posit that strand discrimination in non-methyl-directed MMR is achieved through a structural strategy involving the β-Clamp which is distinct from the chemical strategy employed in prokaryotes like Escherichia coli.

PubMed: 39988319
DOI: 10.1093/nar/gkaf094

Experimental method

X-RAY DIFFRACTION (3.5 Å)