8UN9

Crystal structure of the MrfB exonuclease catalytic core

8UN9 の概要

• エントリーDOI: 10.2210/pdb8un9/pdb
• 分子名称: Exonuclease MrfB, MAGNESIUM ION (3 entities in total)
• 機能のキーワード: exonuclease, dna, hydrolase
• 由来する生物種: Bacillus subtilis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 57284.10

構造登録者

Manthei, K.A.,Nandakumar, J.,Simmons, L.A. (登録日: 2023-10-18, 公開日: 2024-05-01, 最終更新日: 2024-07-03)

主引用文献

Manthei, K.A.,Munson, L.M.,Nandakumar, J.,Simmons, L.A.
Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB.
Nucleic Acids Res., 52:6347-6359, 2024

PubMed Abstract: Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.

PubMed: 38661211
DOI: 10.1093/nar/gkae308

実験手法

X-RAY DIFFRACTION (2.103 Å)