5cot | pdb_00005cot

Structure and mechanism of a eukaryal nick-sealing RNA ligase

spinqualitylabelsall models 5cot, resolution 1.69Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5cot is a 1 chain structure with sequence from Naegleria gruberi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.69Å Ligands: AMP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function D2W2Z5_NAEGR Publication Abstract from PubMed ATP-dependent RNA ligases are agents of RNA repair that join 3'-OH and 5'-PO4 RNA ends. Naegleria gruberi RNA ligase (NgrRnl) exemplifies a family of RNA nick-sealing enzymes found in bacteria, viruses, and eukarya. Crystal structures of NgrRnl at three discrete steps along the reaction pathway-covalent ligase-(lysyl-Nzeta)-AMP*Mn(2+) intermediate; ligase*ATP*(Mn(2+))2 Michaelis complex; and ligase*Mn(2+) complex-highlight a two-metal mechanism of nucleotidyl transfer, whereby (i) an enzyme-bound "catalytic" metal coordination complex lowers the pKa of the lysine nucleophile and stabilizes the transition state of the ATP alpha phosphate; and (ii) a second metal coordination complex bridges the beta- and gamma-phosphates. The NgrRnl N domain is a distinctively embellished oligonucleotide-binding (OB) fold that engages the gamma-phosphate and associated metal complex and orients the pyrophosphate leaving group for in-line catalysis with stereochemical inversion at the AMP phosphate. The unique domain architecture of NgrRnl fortifies the theme that RNA ligases have evolved many times, and independently, by fusions of a shared nucleotidyltransferase domain to structurally diverse flanking modules. The mechanistic insights to lysine adenylylation gained from the NgrRnl structures are likely to apply broadly to the covalent nucleotidyltransferase superfamily of RNA ligases, DNA ligases, and RNA capping enzymes. Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase.,Unciuleac MC, Goldgur Y, Shuman S Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13868-73. doi:, 10.1073/pnas.1516536112. Epub 2015 Oct 28. PMID:26512110 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also RNA ligase

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