8UN9
Crystal structure of the MrfB exonuclease catalytic core
Summary for 8UN9
| Entry DOI | 10.2210/pdb8un9/pdb |
| Descriptor | Exonuclease MrfB, MAGNESIUM ION (3 entities in total) |
| Functional Keywords | exonuclease, dna, hydrolase |
| Biological source | Bacillus subtilis |
| Total number of polymer chains | 2 |
| Total formula weight | 57284.10 |
| Authors | Manthei, K.A.,Nandakumar, J.,Simmons, L.A. (deposition date: 2023-10-18, release date: 2024-05-01, Last modification date: 2024-07-03) |
| Primary citation | 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 Cited by 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: 38661211DOI: 10.1093/nar/gkae308 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.103 Å) |
Structure validation
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