Cullin4-RING Ubiquitin Ligases (Schwefel Lab)

The Schwefel lab is interested in

  • the molecular mechanisms of substrate protein recognition,
  • the cellular consequences of substrate modification with ubiquitin,
  • the interaction of Cullin4-RING ligases with viral proteins, and how these binding processes change the substrate specificity.

In addition, we study the interaction of Cullin4-RING ligases with viral proteins, and how these binding processes change the substrate specificity.

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  • Substrate recognition and specificity modulation of Cullin4-RING ubiquitin ligases.

Substrate recognition and specificity modulation of Cullin4-RING ubiquitin ligases ("Emmy Noether Programme", DFG)

Summary

Cullin4-RING E3 ubiquitin ligases evolved a modular architecture for the targeted modification of cellular proteins with ubiquitin, in order to mark substrates for proteasomal degradation or to induce other regulatory processes, with implications for DNA repair, DNA replication and cell cycle control.

Substrates are specifically recognised by exchangeable receptors (DCAFs, Table 1), which are connected to the Cullin4-RING sub-complex via an adapter protein (DDB1, Figure 1A). This modular architecture of Cullin4-RING ligases ensures proper placement of the substrate for ubiquitin transfer (Figure 1B).

Table 1

Table: Putative DCAFs identified (+) in proteomic screens using DDB1 as bait.

[Englische Übersetzung] DCAF Jin et al. He et al. Angers et al. Higa et al. Human interactome
DCAF1 + + +   +
DCAF2 + + + + +
DCAF3 +   +   +
DCAF4 +   +    
DCAF5 +   +    
DCAF6 +   +   +
DCAF7 +        
DCAF8 +   +    
DCAF9 +   +    
DCAF10 + + +   +
DCAF11 +   +   +
DCAF12 +   +   +
DCAF13 +        
DCAF14 +   +    
DCAF15 +        
DCAF16 +   +    
DCAF17 +        
DCAF19     +    
CSA + + +    
DDB2 + + + +  
DET1/COP1 +/+ -/+ +/- -/+  
DDA1 +   +   +
PWP1   +      
GNB2   +      
KATNB1   +      
RBBP7   +      
FBXW5   +      
FBXW8   +      
NUP43   +      
APG16L   +      
RBBP4   +      
GRWD1   +   +  
WSB1   +      
WSB2   +      
IFRG15     +   +
TRPC4AP     + +  
TLE1-3       +  
WDR26       +  
WDR82       +  
SMU1       +  
RBBP5       +  
WDR5B       +  
POC1B       +  
SNRNP40       +  
WDR61       +  
WDR76       +  
WDR5       +  
PAFAH1B1       +  
NLE1       +  
WDR12       +  
WDR39       +  
WDR53       +  
WDR59       +  
EED       +  
GTF3C2         +

The following issues are addressed in the Schwefel lab on a molecular level:

Figure 1 Schwefel.gif
Figure 1
Modular architecture of the Cullin4-RING E3 ligase complex

A – Two views of the Cullin4-RING E3 ligase assembly. The model was constructed by superposition of the molecular structure of the Cullin4-RBX1-DDB1 subcomplex (PDB 2hye, [3]) with our own DDB1-DCAF1 crystal structure. Components of the assembly and their role are indicated.
B – Schematic model of the ubiquitin transfer process. Specific binding of the substrate protein by the DCAF receptor places the substrate in a position suitable for ubiquitin transfer from ubiquitin-charged E2, which in turn is bound by the RING domain subunit RBX1.
  • How is the substrate receptor DCAF1 integrated in the E3 ligase complex, how are substrate proteins specifically recognised, and what are the consequences for the substrate and the cell?
  • The interaction of DCAF1 with accessory proteins from immunodeficiency viruses will be studied, in order to understand the molecular mechanism of virus-induced DCAF1 specificity modulation and the resulting degradation of antiviral factors. This approach will not only provide insights into viral modification of the Cullin4-RING system, but also contribute to further understanding of retroviral replication.
  • Potential substrates of yet uncharacterised DCAFs will be identified, to gain new insights into Cullin4 receptor specificity and hence into the biology of the Cullin4-RING system.
Dr. David Schwefel
Team
Scientific Background of the Cullin4-RING ubiquitin ligases