8W1D
CRYSTAL STRUCTURE OF DPS-LIKE PROTEIN PA4880 FROM PSEUDOMONAS AERUGINOSA (DIMERIC FORM)
Summary for 8W1D
| Entry DOI | 10.2210/pdb8w1d/pdb |
| Descriptor | DPS-LIKE PROTEIN, FE (II) ION (3 entities in total) |
| Functional Keywords | pa4880, dps protein, metal binding, dna cleavage, metal binding protein |
| Biological source | Pseudomonas aeruginosa PAO1 |
| Total number of polymer chains | 1 |
| Total formula weight | 20353.32 |
| Authors | Lovell, S.,Battaile, K.P.,Rivera, M. (deposition date: 2024-02-15, release date: 2024-05-29, Last modification date: 2024-06-19) |
| Primary citation | Rajapaksha, N.,Yao, H.,Cook, A.,Seibold, S.,Liu, L.,Battaile, K.P.,Fontenot, L.,Donnarumma, F.,Lovell, S.,Rivera, M. Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity. Front Mol Biosci, 11:1390745-1390745, 2024 Cited by PubMed Abstract: We report the biochemical, structural, and functional characterization of the protein coded by gene PA4880 in the PAO1 genome. The PA4880 gene had been annotated as coding a probable bacterioferritin. Our structural work shows that the product of gene PA4880 is a protein that adopts the Dps subunit fold, which oligomerizes into a 12-mer quaternary structure. Unlike Dps, however, the ferroxidase di-iron centers and iron coordinating ligands are buried within each subunit, in a manner identical to that observed in the ferroxidase center of bacterioferritin. Since these structural characteristics correspond to Dps-like proteins, we term the protein as Dps-like, or Pa DpsL. The ferroxidase centers in Pa DpsL catalyze the oxidation of Fe utilizing O or HO as oxidant, and the resultant Fe is compartmentalized in the interior cavity. Interestingly, incubating Pa DpsL with plasmid DNA results in efficient nicking of the DNA and at higher concentrations of Pa DpsL the DNA is linearized and eventually degraded. The nickase and endonuclease activities suggest that Pa DpsL, in addition to participating in the defense of cells against iron-induced toxicity, may also participate in the innate immune mechanisms consisting of restriction endonucleases and cognate methyl transferases. PubMed: 38841187DOI: 10.3389/fmolb.2024.1390745 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.3 Å) |
Structure validation
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