Functional and structural studies of the nucleotide excision repair helicase XPD suggest a polarity for DNA translocation

EMBO J. 2012 Jan 18;31(2):494-502. doi: 10.1038/emboj.2011.374. Epub 2011 Nov 11.

Abstract

The XPD protein is a vital subunit of the general transcription factor TFIIH which is not only involved in transcription but is also an essential component of the eukaryotic nucleotide excision DNA repair (NER) pathway. XPD is a superfamily-2 5'-3' helicase containing an iron-sulphur cluster. Its helicase activity is indispensable for NER and it plays a role in the damage verification process. Here, we report the first structure of XPD from Thermoplasma acidophilum (taXPD) in complex with a short DNA fragment, thus revealing the polarity of the translocated strand and providing insights into how the enzyme achieves its 5'-3' directionality. Accompanied by a detailed mutational and biochemical analysis of taXPD, we define the path of the translocated DNA strand through the protein and identify amino acids that are critical for protein function.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • DNA Helicases / chemistry*
  • DNA Helicases / metabolism
  • DNA Repair
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Protein Binding
  • Protein Conformation
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Structure-Activity Relationship
  • Thermoplasma / enzymology*

Substances

  • Archaeal Proteins
  • DNA, Single-Stranded
  • DNA Helicases

Associated data

  • PDB/4A15