Structure and DNA binding of the human Rtf1 Plus3 domain

Structure. 2008 Jan;16(1):149-59. doi: 10.1016/j.str.2007.10.018.

Abstract

The yeast Paf1 complex consists of Paf1, Rtf1, Cdc73, Ctr9, and Leo1 and regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. We provide structural insight into the Paf1 complex with the NMR structure of the conserved and functionally important Plus3 domain of human Rtf1. A predominantly beta-stranded subdomain displays structural similarity to Dicer/Argonaute PAZ domains and to Tudor domains. We further demonstrate that the highly basic Rtf1 Plus3 domain can interact in vitro with single-stranded DNA via residues on the rim of the beta sheet, reminiscent of siRNA binding by PAZ domains, but did not detect binding to double-stranded DNA or RNA. We discuss the potential role of Rtf1 Plus3 ssDNA binding during transcription elongation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Conserved Sequence
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / genetics
  • DNA, Single-Stranded / metabolism
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acids / chemistry
  • Nucleic Acids / metabolism
  • Protein Conformation
  • Proton-Translocating ATPases
  • Sequence Alignment
  • Suppressor Factors, Immunologic / chemistry*
  • Suppressor Factors, Immunologic / genetics
  • Suppressor Factors, Immunologic / metabolism*
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics*
  • Transcription, Genetic

Substances

  • DNA, Single-Stranded
  • Nucleic Acids
  • Suppressor Factors, Immunologic
  • Transcription Factors
  • RTF1 protein, human
  • ATP6V0A2 protein, human
  • Proton-Translocating ATPases

Associated data

  • PDB/2BZE