T4 RNA ligase 2 (Rnl2)

From Proteopedia

Revision as of 22:30, 15 February 2010

T4 RNA ligase 2 (Rnl2):

Overview:

T4 RNA ligase 2 (Rnl2) (1-249) is a T4 bacteriophage ligase, which functions to counter bacterial defence by repairing broken anticodon loops of tRNA coding for lysine, caused by PrrC, which is nessessary for viral replication and proliferation. Note that the structure shown is based on the truncated enzyme form (1-249) where the total chain length of Rnl2 is 334 residues. The overall structure, at 100K, pH 8.5, consists of a single chain polymer (233 residues + 15 His tag residues) composed of 2, 6 antiparalel stranded, beta sheets and 7 alpha helices. The structure contains an adenosine monophosphate ligand in its active site. The enzyme contains 5 nucleotidyl transferase motifs, I, III, IIIa, IV and V Outlined in Figure 1. which are all involved either directly for indirectly with the function of the active site.

Protein function:

Although this protein is designed to counteract the bacterial host’s defence mechanisms against the virus, its activity as a ligase is analogous to tRNA splicing (introns removed from anticodon loop) and RNA editing by several different kinds of RNA editing ligases (REL)s. Therefore it have been grouped into a subfamily of RNA ligases including REL-1 which is essential for Trypanosoma, a monophyletic group of unicellular paracitic flagella protozoa that causes sleeping sickness, survival. Another commonality shared between RNA ligases as well as DNA ligases and capping enzymes is the fact that the mechanism by which they function involves the formation of a covalent enzyme-(lysyl-N)-NMP intermediate prior to the formation of the phophodiester bond between 5’ and 3’ ends of RNA strands. Hence these groups have been classified as a super family of enzymes characteristic of the above intermediate.

The mechanism for the formation of this intermediate and the phosphodiester bond resulting in RNA strand repair is outlined below. First ATP reacts with the active site of Rln2. Adenosine mono phosphate binds to the accompanied by the release of inorganic phosphate which provides the energy. The adenylate binds at the bottom of the where it is squished between the aromatic rings of of motif IIIa of motif III and of of motif I. The specificity of Rln2 for ATP as opposed to other NTP substrates in this step are thought to be attributed to hydrogen bonding between backbone residues and the Adenine base. Such bonds occur between: the exocyclic 6-amino group and main chain carbonyl of Glu 34, N1 and Lys 209 (water mediated), (Figure 1). The πstacking between Phe 119 and the adenylate base is through to be critical for the transfer of the phophate from the 5’ end of the RNA strand to the 3’ OH end of the RNA strand to form the phosphodiester bond.

Current Refences: Ho et al. 2004 Structure and Mechanism of RNA Ligase. 12:327-339