Structural insight into poly(A) binding and catalytic mechanism of human PARN

EMBO J. 2005 Dec 7;24(23):4082-93. doi: 10.1038/sj.emboj.7600869. Epub 2005 Nov 10.

Abstract

Poly(A)-specific ribonuclease (PARN) is a processive, poly(A)-specific 3' exoribonuclease. The crystal structure of C-terminal truncated human PARN determined in two states (free and RNA-bound forms) reveals that PARNn is folded into two domains, an R3H domain and a nuclease domain similar to those of Pop2p and epsilon186. The high similarity of the active site structures of PARNn and epsilon186 suggests that they may have a similar catalytic mechanism. PARNn forms a tight homodimer, with the R3H domain of one subunit partially enclosing the active site of the other subunit and poly(A) bound in a deep cavity of its nuclease domain in a sequence-nonspecific manner. The R3H domain and, possibly, the cap-binding domain are involved in poly(A) binding but these domains alone do not appear to contribute to poly(A) specificity. Mutations disrupting dimerization abolish both the enzymatic and RNA-binding activities, suggesting that the PARN dimer is a structural and functional unit. The cap-binding domain may act in concert with the R3H domain to amplify the processivity of PARN.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / metabolism*
  • Amino Acid Sequence
  • Catalytic Domain
  • Crystallography, X-Ray
  • Dimerization
  • Exoribonucleases / chemistry*
  • Exoribonucleases / metabolism*
  • Humans
  • Molecular Sequence Data
  • Polymers / metabolism*
  • Protein Binding
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Structural Homology, Protein

Substances

  • Polymers
  • polyadenosine
  • Exoribonucleases
  • poly(A)-specific ribonuclease
  • Adenosine

Associated data

  • PDB/2A1R
  • PDB/2A1S