5TT5
Escherichia coli LigA (K115M) in complex with NAD+
Summary for 5TT5
| Entry DOI | 10.2210/pdb5tt5/pdb |
| Related | 5TT6 |
| Descriptor | DNA ligase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ZINC ION, ... (5 entities in total) |
| Functional Keywords | metal catalysis, covalent nucleotidyltransferase, lysyl-amp, ligase |
| Biological source | Escherichia coli (strain K12) |
| Total number of polymer chains | 1 |
| Total formula weight | 76931.82 |
| Authors | Goldgur, Y.,Unciuleac, M.-C.,Shuman, S.H. (deposition date: 2016-11-01, release date: 2017-03-08, Last modification date: 2023-10-04) |
| Primary citation | Unciuleac, M.C.,Goldgur, Y.,Shuman, S. Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD(+)-dependent polynucleotide ligases. Proc. Natl. Acad. Sci. U.S.A., 114:2592-2597, 2017 Cited by PubMed Abstract: Polynucleotide ligases comprise a ubiquitous superfamily of nucleic acid repair enzymes that join 3'-OH and 5'-PO DNA or RNA ends. Ligases react with ATP or NAD and a divalent cation cofactor to form a covalent enzyme-(lysine-Nζ)-adenylate intermediate. Here, we report crystal structures of the founding members of the ATP-dependent RNA ligase family (T4 RNA ligase 1; Rnl1) and the NAD-dependent DNA ligase family ( LigA), captured as their respective Michaelis complexes, which illuminate distinctive catalytic mechanisms of the lysine adenylylation reaction. The 2.2-Å Rnl1•ATP•(Mg) structure highlights a two-metal mechanism, whereby: a ligase-bound "catalytic" Mg(HO) coordination complex lowers the p of the lysine nucleophile and stabilizes the transition state of the ATP α phosphate; a second octahedral Mg coordination complex bridges the β and γ phosphates; and protein elements unique to Rnl1 engage the γ phosphate and associated metal complex and orient the pyrophosphate leaving group for in-line catalysis. By contrast, the 1.55-Å LigA•NAD•Mg structure reveals a one-metal mechanism in which a ligase-bound Mg(HO) complex lowers the lysine p and engages the NAD α phosphate, but the β phosphate and the nicotinamide nucleoside of the nicotinamide mononucleotide (NMN) leaving group are oriented solely via atomic interactions with protein elements that are unique to the LigA clade. The two-metal versus one-metal dichotomy demarcates a branchpoint in ligase evolution and favors LigA as an antibacterial drug target. PubMed: 28223499DOI: 10.1073/pnas.1619220114 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.552 Å) |
Structure validation
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