5B42

Crystal structure of the C-terminal endonuclease domain of Aquifex aeolicus MutL.

Summary for 5B42

• Entry DOI: 10.2210/pdb5b42/pdb
• Descriptor: DNA mismatch repair protein MutL, CADMIUM ION, DI(HYDROXYETHYL)ETHER, ... (4 entities in total)
• Functional Keywords: mismatch repair, endonuclease, cadmium, dna binding protein
• Biological source: Aquifex aeolicus (strain VF5)
• Total number of polymer chains: 1
• Total formula weight: 13238.97

Authors

Fukui, K.,Baba, S.,Kumasaka, T.,Yano, T. (deposition date: 2016-03-30, release date: 2016-07-13, Last modification date: 2024-03-20)

Primary citation

Fukui, K.,Baba, S.,Kumasaka, T.,Yano, T.
Structural Features and Functional Dependency on beta-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL
J.Biol.Chem., 291:16990-17000, 2016

PubMed Abstract: In early reactions of DNA mismatch repair, MutS recognizes mismatched bases and activates MutL endonuclease to incise the error-containing strand of the duplex. DNA sliding clamp is responsible for directing the MutL-dependent nicking to the newly synthesized/error-containing strand. In Bacillus subtilis MutL, the β-clamp-interacting motif (β motif) of the C-terminal domain (CTD) is essential for both in vitro direct interaction with β-clamp and in vivo repair activity. A large cluster of negatively charged residues on the B. subtilis MutL CTD prevents nonspecific DNA binding until β clamp interaction neutralizes the negative charge. We found that there are some bacterial phyla whose MutL endonucleases lack the β motif. For example, the region corresponding to the β motif is completely missing in Aquifex aeolicus MutL, and critical amino acid residues in the β motif are not conserved in Thermus thermophilus MutL. We then revealed the 1.35 Å-resolution crystal structure of A. aeolicus MutL CTD, which lacks the β motif but retains the metal-binding site for the endonuclease activity. Importantly, there was no negatively charged cluster on its surface. It was confirmed that CTDs of β motif-lacking MutLs, A. aeolicus MutL and T. thermophilus MutL, efficiently incise DNA even in the absence of β-clamp and that β-clamp shows no detectable enhancing effect on their activity. In contrast, CTD of Streptococcus mutans, a β motif-containing MutL, required β-clamp for the digestion of DNA. We propose that MutL endonucleases are divided into three subfamilies on the basis of their structural features and dependence on β-clamp.

PubMed: 27369079
DOI: 10.1074/jbc.M116.739664

Experimental method

X-RAY DIFFRACTION (1.35 Å)