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

Publication Type:

Journal Article


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


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


<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>