RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.

Publication Type:

Journal Article

Authors:

Nandakumar, Jayakrishnan; Shuman, Stewart; Lima, Christopher D

Source:

Cell, Volume 127, Issue 1, p.71-84 (2006)

Keywords:

Adenosine Monophosphate, Adenosine Triphosphate, Base Sequence, Binding Sites, Crystallography, X-Ray, DNA Ligase ATP, DNA Ligases, DNA Mutational Analysis, Humans, Models, Molecular, Molecular Sequence Data, Molecular Structure, Nucleic Acid Conformation, Protein Structure, Tertiary, RNA, RNA Ligase (ATP), Substrate Specificity, Viral Proteins

Abstract:

<p>T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligases exemplify a family of RNA repair enzymes that seal 3'OH/5'PO(4) nicks in duplex RNAs via ligase adenylylation (step 1), AMP transfer to the nick 5'PO(4) (step 2), and attack by the nick 3'OH on the 5'-adenylylated strand to form a phosphodiester (step 3). Crystal structures are reported for Rnl2 at discrete steps along this pathway: the covalent Rnl2-AMP intermediate; Rnl2 bound to an adenylylated nicked duplex, captured immediately following step 2; and Rnl2 at an adenylylated nick in a state poised for step 3. These structures illuminate the stereochemistry of nucleotidyl transfer and reveal how remodeling of active-site contacts and conformational changes propel the ligation reaction forward. Mutational analysis and comparison of nick-bound structures of Rnl2 and human DNA ligase I highlight common and divergent themes of substrate recognition that can explain their specialization for RNA versus DNA repair.</p>