Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase Journal Article

   


Authors: Unciuleac, M. C.; Goldgur, Y.; Shuman, S.
Article Title: Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase
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-NΧ)•AMP.Mn2+ intermediate; ligase•ATP•(Mn2+)2 Michaelis complex; and ligase•Mn2+ 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.
Keywords: nonhuman; conference paper; protein domain; complex formation; molecular evolution; amino terminal sequence; crystal structure; catalysis; adenosine triphosphate; crystallization; enzyme specificity; enzyme binding; enzyme structure; oligonucleotide; lysine; enzyme mechanism; stereochemistry; nucleophile; adenosine phosphate; adenylation; rna repair; phase transition; manganese; adenine nucleotide; coordination compound; rna ligase; naegleria gruberi; pyrophosphate; priority journal; metal complex; covalent nucleotidyltransferase; lysyl-amp
Journal Title: Proceedings of the National Academy of Sciences of the United States of America
Volume: 112
Issue: 45
ISSN: 0027-8424
Publisher: National Academy of Sciences  
Date Published: 2015-11-10
Start Page: 13868
End Page: 13873
Language: English
DOI: 10.1073/pnas.1516536112
PROVIDER: scopus
PUBMED: 26512110
PMCID: PMC4653202
DOI/URL:

http://www.scopus.com/inward/record.url?eid=2-s2.0-84946925819&partnerID=40&md5=72f7a6e382ca6f35cb5ac2b4fa16d709
Notes: Export Date: 2 December 2015 -- Source: Scopus
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MSK Authors
  1. Stewart H Shuman
    546 Shuman
  2. Mihaela Carmen Sandu
    19 Sandu
  3. Yehuda Goldgur
    42 Goldgur
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