6N0V

tRNA ligase

Summary for 6N0V

• Entry DOI: 10.2210/pdb6n0v/pdb
• Descriptor: tRNA ligase, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: trna, rna ligase, nucleotidyltransferase, n6-amp-lysine intermediate, ligase
• Biological source: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
• Total number of polymer chains: 2
• Total formula weight: 92908.17

Authors

Banerjee, A.,Goldgur, Y.,Shuman, S. (deposition date: 2018-11-07, release date: 2019-01-09, Last modification date: 2019-12-04)

Primary citation

Banerjee, A.,Ghosh, S.,Goldgur, Y.,Shuman, S.
Structure and two-metal mechanism of fungal tRNA ligase.
Nucleic Acids Res., 47:1428-1439, 2019

PubMed Abstract: Fungal tRNA ligase (Trl1) is an essential enzyme that repairs RNA breaks with 2',3'-cyclic-PO4 and 5'-OH ends inflicted during tRNA splicing and non-canonical mRNA splicing in the fungal unfolded protein response. Trl1 is composed of C-terminal cyclic phosphodiesterase (CPD) and central GTP-dependent polynucleotide kinase (KIN) domains that heal the broken ends to generate the 3'-OH,2'-PO4 and 5'-PO4 termini required for sealing by an N-terminal ATP-dependent ligase domain (LIG). Here we report crystal structures of the Trl1-LIG domain from Chaetomium thermophilum at two discrete steps along the reaction pathway: the covalent LIG-(lysyl-Nζ)-AMP•Mn2+ intermediate and a LIG•ATP•(Mn2+)2 Michaelis complex. The structures highlight a two-metal mechanism whereby a penta-hydrated metal complex stabilizes the transition state of the ATP α phosphate and a second metal bridges the β and γ phosphates to help orient the pyrophosphate leaving group. A LIG-bound sulfate anion is a plausible mimetic of the essential RNA terminal 2'-PO4. Trl1-LIG has a distinctive C-terminal domain that instates fungal Trl1 as the founder of an Rnl6 clade of ATP-dependent RNA ligase. We discuss how the Trl1-LIG structure rationalizes the large body of in vivo structure-function data for Saccharomyces cerevisiae Trl1.

PubMed: 30590734
DOI: 10.1093/nar/gky1275

Experimental method

X-RAY DIFFRACTION (2.502 Å)