The thalidomide-binding domain of cereblon defines the CULT domain family and is a new member of the β-tent fold

PLoS Comput Biol. 2015 Jan 8;11(1):e1004023. doi: 10.1371/journal.pcbi.1004023. eCollection 2015 Jan.

Abstract

Despite having caused one of the greatest medical catastrophies of the last century through its teratogenic side-effects, thalidomide continues to be an important agent in the treatment of leprosy and cancer. The protein cereblon, which forms an E3 ubiquitin ligase compex together with damaged DNA-binding protein 1 (DDB1) and cullin 4A, has been recently indentified as a primary target of thalidomide and its C-terminal part as responsible for binding thalidomide within a domain carrying several invariant cysteine and tryptophan residues. This domain, which we name CULT (cereblon domain of unknown activity, binding cellular ligands and thalidomide), is also found in a family of secreted proteins from animals and in a family of bacterial proteins occurring primarily in δ-proteobacteria. Its nearest relatives are yippee, a highly conserved eukaryotic protein of unknown function, and Mis18, a protein involved in the priming of centromeres for recruitment of CENP-A. Searches for distant homologs point to an evolutionary relationship of CULT, yippee, and Mis18 to proteins sharing a common fold, which consists of two four-stranded β-meanders packing at a roughly right angle and coordinating a zinc ion at their apex. A β-hairpin inserted into the first β-meander extends across the bottom of the structure towards the C-terminal edge of the second β-meander, with which it forms a cradle-shaped binding site that is topologically conserved in all members of this fold. We name this the β-tent fold for the striking arrangement of its constituent β-sheets. The fold has internal pseudosymmetry, raising the possibility that it arose by duplication of a subdomain-sized fragment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing
  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Carrier Proteins / chemistry
  • Drosophila
  • Drosophila Proteins / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Peptide Hydrolases / chemistry*
  • Peptide Hydrolases / metabolism*
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Thalidomide / chemistry*
  • Thalidomide / metabolism*
  • Ubiquitin-Protein Ligases

Substances

  • Adaptor Proteins, Signal Transducing
  • CRBN protein, human
  • Carrier Proteins
  • Drosophila Proteins
  • Yippee protein, Drosophila
  • Thalidomide
  • Ubiquitin-Protein Ligases
  • Peptide Hydrolases

Grants and funding

This study was supported by institutional funds of the Max Planck Society (http://www.mpg.de/) to ANL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.