6NVP
Crystal structure of Pseudomonas putida nuclease MPE
Summary for 6NVP
| Entry DOI | 10.2210/pdb6nvp/pdb |
| Related | 6NV0 |
| Descriptor | Nuclease MPE, MANGANESE (II) ION (3 entities in total) |
| Functional Keywords | binuclear metallo-phosphodiesterase/nuclease, dna binding protein |
| Biological source | Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) |
| Total number of polymer chains | 1 |
| Total formula weight | 24507.96 |
| Authors | Goldgur, Y.,Shuman, S.,Ejaz, A. (deposition date: 2019-02-05, release date: 2019-03-27, Last modification date: 2024-03-13) |
| Primary citation | Ejaz, A.,Goldgur, Y.,Shuman, S. Activity and structure ofPseudomonas putidaMPE, a manganese-dependent single-strand DNA endonuclease encoded in a nucleic acid repair gene cluster. J.Biol.Chem., 294:7931-7941, 2019 Cited by PubMed Abstract: A recently identified and widely prevalent prokaryal gene cluster encodes a suite of enzymes with imputed roles in nucleic acid repair. The enzymes are as follows: MPE, a DNA endonuclease; Lhr-Core, a 3'-5' DNA helicase; LIG, an ATP-dependent DNA ligase; and Exo, a metallo-β-lactamase-family nuclease. Bacterial and archaeal MPE proteins belong to the binuclear metallophosphoesterase superfamily that includes the well-studied DNA repair nucleases Mre11 and SbcD. Here, we report that the MPE protein is a manganese-dependent DNA endonuclease that incises either linear single strands or the single-strand loops of stem-loop DNA structures. MPE has feeble activity on duplex DNA. A crystal structure of MPE at 2.2 Å resolution revealed that the active site includes two octahedrally coordinated manganese ions. Seven signature amino acids of the binuclear metallophosphoesterase superfamily serve as the enzymic metal ligands in MPE: Asp, His, Asp, Asn, His, His, and His A swath of positive surface potential on either side of the active site pocket suggests a binding site for the single-strand DNA substrate. The structure of MPE differs from Mre11 and SbcD in several key respects: (i) MPE is a monomer, whereas Mre11 and SbcD are homodimers; (ii) MPE lacks the capping domain present in Mre11 and SbcD; and (iii) the topology of the β sandwich that comprises the core of the metallophosphoesterase fold differs in MPE Mre11 and SbcD. We surmise that MPE exemplifies a novel clade of DNA endonuclease within the binuclear metallophosphoesterase superfamily. PubMed: 30894417DOI: 10.1074/jbc.RA119.008049 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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