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

Cell. 2006 Oct 6;127(1):71-84. doi: 10.1016/j.cell.2006.08.038.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

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

Substances

  • LIG1 protein, human
  • Viral Proteins
  • Adenosine Monophosphate
  • RNA
  • Adenosine Triphosphate
  • DNA Ligases
  • DNA Ligase ATP
  • RNA Ligase (ATP)
  • bacteriophage T4 RNA ligase 2

Associated data

  • PDB/2HVQ
  • PDB/2HVR
  • PDB/2HVS