A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1

FEBS J. 2016 Jun;283(11):2004-17. doi: 10.1111/febs.13734. Epub 2016 Apr 28.


The ubiquitin-binding zinc finger (UBZ) is a type of zinc-coordinating β-β-α fold domain found mainly in proteins involved in DNA repair and transcriptional regulation. Here, we report the crystal structure of the UBZ domain of Y-family DNA polymerase (pol) η and the crystal structure of the complex between the UBZ domain of Werner helicase-interacting protein 1 (WRNIP1) and ubiquitin, crystallized using the GFP fusion technique. In contrast to the pol η UBZ, which has been proposed to bind ubiquitin via its C-terminal α-helix, ubiquitin binds to a novel surface of WRNIP1 UBZ composed of the first β-strand and the C-terminal α-helix. In addition, we report the structure of the tandem UBZ domains of Tax1-binding protein 1 (TAX1BP1) and show that the second UBZ of TAX1BP1 binds ubiquitin, presumably in a manner similar to that of WRNIP1 UBZ. We propose that UBZ domains can be divided into at least two different types in terms of the ubiquitin-binding surfaces: the pol η type and the WRNIP1 type.

Database: Structural data are available in the Protein Data Bank under accession numbers 3WUP (pol η UBZ), 3VHS (WRNIP1 UBZ), 3VHT (GFP-WRNIP1/ubiquitin), 4Z4K (TAX1BP1 UBZ1 + 2), and 4Z4M (TAX1BP1 UBZ2).

Keywords: TAX1BP1; WRNIP1; green fluorescent protein; pol η; ubiquitin-binding zinc finger.

Publication types

  • Editorial

MeSH terms

  • ATPases Associated with Diverse Cellular Activities
  • Carrier Proteins / chemistry*
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism
  • Crystallography, X-Ray
  • DNA Repair / genetics
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Humans
  • Protein Binding / genetics
  • Protein Conformation, alpha-Helical
  • Protein Folding
  • Ubiquitin / chemistry*
  • Ubiquitin / genetics
  • Ubiquitin / metabolism
  • Zinc Fingers / genetics


  • Carrier Proteins
  • DNA-Binding Proteins
  • Ubiquitin
  • WRNIP1 protein, human
  • ATPases Associated with Diverse Cellular Activities