7udi | pdb_00007udi

Full-length dimer of DNA-Damage Response Protein C from Deinococcus radiodurans

spinqualitylabelsall models 7udi, resolution 2.24Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7udi is a 2 chain structure with sequence from Deinococcus radiodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.24Å Ligands: MSE, SO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function DDRC_DEIRA Appears to contribute to D.radiodurans capacity to survive exposure to ionizing radiation (PubMed:15454524). Likely functions as a DNA damage-induced nucleoid-associated protein (NAP) that contributes to the enhanced level of nucleoid compaction after irradiation by bridging DNA duplexes, thereby limiting the dispersion of the fragmented genome immediately after irradiation to facilitate subsequent DNA repair. In vitro, binds both ssDNA and dsDNA, and is able to compact circular DNA, circularize linear DNA, anneal complementary DNA strands and protect DNA from nucleases (PubMed:28542368, PubMed:35801857). Publication Abstract from PubMed The bacterium Deinococcus radiodurans is known to survive high doses of DNA damaging agents. This resistance is the result of robust antioxidant systems which protect efficient DNA repair mechanisms that are unique to Deinococcus species. The protein DdrC has been identified as an important component of this repair machinery. DdrC is known to bind to DNA in vitro and has been shown to circularize and compact DNA fragments. The mechanism and biological relevance of this activity is poorly understood. Here, we show that the DdrC homodimer is a lesion-sensing protein that binds to two single-strand (ss) or double-strand (ds) breaks. The immobilization of DNA breaks in pairs consequently leads to the circularization of linear DNA and the compaction of nicked DNA. The degree of compaction is directly proportional with the number of available nicks. Previously, the structure of the DdrC homodimer was solved in an unusual asymmetric conformation. Here, we solve the structure of DdrC under different crystallographic environments and confirm that the asymmetry is an endogenous feature of DdrC. We propose a dynamic structural mechanism where the asymmetry is necessary to trap a pair of lesions. We support this model with mutant disruption and computational modeling experiments. DdrC, a unique DNA repair factor from D. radiodurans, senses and stabilizes DNA breaks through a novel lesion-recognition mechanism.,Szabla R, Li M, Warner V, Song Y, Junop M Nucleic Acids Res. 2024 Jul 22:gkae635. doi: 10.1093/nar/gkae635. PMID:39036966 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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