6n0v | pdb_00006n0v

tRNA ligase

spinqualitylabelsall models 6n0v, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6n0v is a 2 chain structure with sequence from Chatd. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MN NonStd Res: APK Gene: CTHT_0034810 (CHATD) Activity: RNA ligase (ATP), with EC number 6.5.1.3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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-Nzeta)-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 alpha phosphate and a second metal bridges the beta and gamma 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. Structure and two-metal mechanism of fungal tRNA ligase.,Banerjee A, Ghosh S, Goldgur Y, Shuman S Nucleic Acids Res. 2018 Dec 22. pii: 5258021. doi: 10.1093/nar/gky1275. PMID:30590734 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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