5COT

Structure and mechanism of a eukaryal nick-sealing RNA ligase

Summary for 5COT

• Entry DOI: 10.2210/pdb5cot/pdb
• Related: 5COU 5COV
• Descriptor: Naegleria gruberi RNA ligase, ADENOSINE MONOPHOSPHATE, UNKNOWN ATOM OR ION, ... (4 entities in total)
• Functional Keywords: rna repair, adenylyltransferase, ligase
• Biological source: Naegleria gruberi (Amoeba)
• Total number of polymer chains: 1
• Total formula weight: 39033.36

Authors

Unciuleac, M.C.,Goldgur, Y.,Shuman, S. (deposition date: 2015-07-20, release date: 2015-10-28, Last modification date: 2024-11-06)

Primary citation

Unciuleac, M.C.,Goldgur, Y.,Shuman, S.
Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase.
Proc.Natl.Acad.Sci.USA, 112:13868-13873, 2015

PubMed Abstract: 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-Nζ)-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 α phosphate; and (ii) a second metal coordination complex bridges the β- and γ-phosphates. The NgrRnl N domain is a distinctively embellished oligonucleotide-binding (OB) fold that engages the γ-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.

PubMed: 26512110
DOI: 10.1073/pnas.1516536112

Experimental method

X-RAY DIFFRACTION (1.69 Å)