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Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery.

Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes. Conserved from yeast to human, the DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair, DNA replication and transcription, and can also be subverted by pathogenic viruses to benefit viral infection. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses one beta-propeller domain for cullin scaffold binding and a variably attached separate double-beta-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes.

Pubmed ID: 16964240


  • Angers S
  • Li T
  • Yi X
  • MacCoss MJ
  • Moon RT
  • Zheng N



Publication Data

October 5, 2006

Associated Grants


Mesh Terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding Sites
  • Carrier Proteins
  • Crystallography, X-Ray
  • Cullin Proteins
  • DNA-Binding Proteins
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Pliability
  • Protein Binding
  • Protein Structure, Quaternary
  • Proteomics
  • Structure-Activity Relationship
  • Substrate Specificity
  • Ubiquitin
  • Ubiquitin-Protein Ligases