Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2.

ABSTRACT:

Background

RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular biology. Here we report the identification of a divergent RNA ligase 2 (DpRNL) from Diplonema papillatum (Diplonemea), a member of the kinetoplastids' sister group.

Methods

We identified DpRNL with methods based on sensitive hidden Markov Model. Then, using homology modeling and molecular dynamics simulations, we established a three dimensional structure model of DpRNL complexed with ATP and Mg2+.

Results

The 3D model of Diplonema was compared with available crystal structures from

SUBMITTER: Moreira S 

PROVIDER: S-EPMC4599027 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature