Fungal tRNA ligase
| Fungal tRNA ligase is an enzyme that attaches the appropriate amino acid onto its tRNA. It is done through esterfication or it is precursor to one of its compatible amino acid tRNAs to form an aminoacyl-tRNA.
Background Information
Transfer ribonucleic acid is a protein molecule that are between 70-90 nucleotides long. It is a type of RNA that helps translate messenger RNA sequences into the form of nonfunctional and functional proteins.
TRNAs which are ribonucleic acids and are capable of forming bonds with mRNA (hydrogen bonds) and amino acids (ester linkages). The ester linkage with the amino acid is one of the most important parts of the tRNA due to the anticodon and the 3’ hydroxyl group. These bonding help to bring amino acids and mRNAs together in the process known as translation. During translation, tRNA functions at specific sites in the ribosome. At this time tRNAs read the messages received from nucleic acid and translate them into proteins known as amino acids These amino acids are made by individual codons.
TRNA base pairs with three nucleotides on a mRNA chain. These three nucleotides are known as codons. In this process there is a corresponding strand or sequence that has an anticodon. When the anticodon and the codon is paired, this helps bring specificity to the process of translation.
TRNAs can be classified based on the amino acids they carry and grouped based on their anticodon. There are about 20 different known tRNAs. There are 64 possible codons that can be translated by tRNA and give us the 20 amino acids and the 3 codes for stopping translation.
Another important structure on the tRNA is the arms. There is a T-arm and D-arm. The D and T arms and the anticodon loop is the regions on the protein that looks like a cloverleaf. When folded into its tertiary structure and in a L-shape, the acceptor stem and the t-arm form a helix that extends while the anticodon and the D-arm forms another helix. These helices are perpendicular to each other allowing the D-arm and the T-arm are close to each other, but the anticodon loop and the acceptor arms are on opposite sides of the molecule.
Referenced Paper Information
In the paper the study focused on the fungal ligase (Trl1) enzyme. This enzyme is important in the repairs of RNA breaks with 2’,3’-cyclic-〖PO〗_4 and 5’-OH ends that have been damaged during the splicing that takes place during the fungal unfolded protein response. These enzymes are made up of CPDs which are cyclic phosphodiesterase and KINs which are central GTP-dependent polynucleotide kinase. These proteins correct the damaged ends. This causes 3’-OH and, 2’-〖PO〗_4 and 5’-〖PO〗_4 to generate. These are required for sealing by a terminal ATP-dependent ligase domain. In this scene the ATP binding pocket with subunits labeled So, this paper focused on the crystallized Trl1-LIG domain from a fungus called Cheatomium thermophililium at two steps along the reaction pathway. These pathways are the covalent LIG-(lysyl-N)-AMP*〖Mn〗^(2+)intermediate Min ion labeled and a LIG*ATP*(〖〖Mn〗^(2+))〗_2 Michaelis complex. The importance of these structures is due to the fact that they point out two-metal mechanism where a pentahydrated metal complex helps to stabilize the transition state of ATP α phosphate and the second metal bridges are β and γ phosphates ATP and Min labeled and coloered. These helps orient the pyrophosphate leaving group. A memetic of RNA terminal 2’-PO4 is the LIG bound sulfate anion. Trl1-LIG instates fungal Trl1 as the original of the Rnl6 clade of ATP-dependent RNA ligase. This Trl-LIG has a special C-terminal that is distinctive C-terminal domain. Over all the study was to see how the Trl-LIG structure supports the large body of in vivo structure-function data for Saccharomyces cerevisiae Trl1.
The goal of this experiment was to determine the structure of the RNA ligase (LIG) domain of a fungal Trl1. In the first reaction the LIG react with ATP to form a covalent LIG-(lysyl-N)-AMP intermediate. This causes a displacement to a pyrophosphate. In the second reaction LIG transfers AMP to 5’-〖PO〗^4 RNA terminus. This helps to form a RNA-adenylate intermediate (A_(5^' pp5') RNA). The third reaction is where the LIG directs the attack of an RNA 3’-OH an the AppRNA to form splice junction and displaces the AMP. This is a feature well defined of the Trl1-LIG.
Studies help educate scientist on fungal tRNA splicing enzymology. It helps provide the structure of a catalytically active ligase domain of Trl1. Trl1-LIG <scene name='75/752264/Fungal_trna_ligase/3'>
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</scene> imitates a new RNA clade.
This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
ATP binding pocket with subunits labeled
ATP binding pocket with Min and ATP labeled
ATP and Min labeled and coloered
Min ion labeled
References
1) Shuman,S. and Lima,C.D. (2004) The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr. Opin. Struct. Biol., 14, 757–764.
2) Banerjee, A. Ghosh, S. Goldgur, Y. and Shuman, S. (2018) Structure and two-metal mechanism of fungal tRNA ligase. Nucleic Acid Research, 2019, Vol 47, No.3 doi:10.1093lnarlgky1275
