title: A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.
abstract: 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.
  
  
  
  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).
authors.affiliation: Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Suzuki
authors.affiliation: Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.|Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.|Departement of Biophysics, Faculty of Science, Cairo University, Giza, Egypt.|Cardiovascular Research institute, the University of California at San Francisco, CA, USA.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Rohaim
authors.affiliation: Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.|Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
authors.forename: Ryuichi
authors.initials: R
authors.lastname: Kato
authors.affiliation: Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt (Main), Germany.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dikic
authors.affiliation: Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.|Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.|Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.|Department of Structural Biology, School of Medicine, Stanford University, CA, USA.
authors.forename: Soichi
authors.initials: S
authors.lastname: Wakatsuki
authors.affiliation: Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.|Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
authors.forename: Masato
authors.initials: M
authors.lastname: Kawasaki
mesh_terms: D000074183:ATPases Associated with Diverse Cellular Activities; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray; D004260:DNA Repair / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D011485:Protein Binding / Q000235:genetics; D000072756:Protein Conformation, alpha-Helical; D017510:Protein Folding; D025801:Ubiquitin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016335:Zinc Fingers / Q000235:genetics
chemical_list: D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D025801:Ubiquitin; C430237:WRNIP1 protein, human; D000074183:ATPases Associated with Diverse Cellular Activities
keywords: TAX1BP1; WRNIP1; green fluorescent protein; pol η; ubiquitin-binding zinc finger