The DDB1–DCAF1–Vpr–UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction

Abstract

The HIV-1 accessory protein Vpr is required for efficient viral infection of macrophages and promotion of viral replication in T cells. Vpr’s biological activities are closely linked to the interaction with human DCAF1, a cellular substrate receptor of the Cullin4–RING E3 ubiquitin ligase (CRL4) of the host ubiquitin–proteasome-mediated protein degradation pathway. The molecular details of how Vpr usurps the protein degradation pathway have not been delineated. Here we present the crystal structure of the DDB1–DCAF1–HIV-1–Vpr–uracil-DNA glycosylase (UNG2) complex. The structure reveals how Vpr engages with DCAF1, creating a binding interface for UNG2 recruitment, in a manner distinct from the recruitment of SAMHD1 by Vpx protein for degradation by Vpx proteins. Vpr and Vpx use similar N-terminal and helical regions to bind the substrate receptor, whereas different regions target the specific cellular substrates. Furthermore, Vpr uses molecular mimicry of DNA by a variable loop for specific recruitment of the UNG2 substrate.

Nuclear Magnetic Resonance Structure of the Human Polyoma JC Virus Agnoprotein

“…Our group has extensively studied the structural properties of Vpr by NMR and determined its structure using nonphysiological conditions, including 30% TFE or acetonitrile, low pH (pH 3.0) and relatively high temperature (50°C) [Morellet et al, ]. Recently, the structure of Vpr was determined again by co‐crystallization studies [Wu et al, ]. This new crystallographic structure of Vpr exactly matches with the one obtained by our group by NMR under nonphysiological conditions.…”

Making Sense of Multifunctional Proteins: Human Immunodeficiency Virus Type 1 Accessory and Regulatory Proteins and Connections to Transcription

“…This model is supported by the fact that DDB1 knockdown alone causes cells to arrest in G 2 (115, 118) and DCAF1 knockdown causes G 1 and G 2 arrests (113). A recent crystal structure of UNG2-Vpr-DCAF1-DDB1 complex supports this model, highlighting that Vpr binds to DCAF1 on the typical DCAF substrate interaction surface, potentially occluding the recruitment of normal substrates (119). UNG2 appears to be a neo-substrate for DCAF1, as Vpr adapts UNG2 to the ligase complex, providing the entirety of the interaction surface.…”

WD40 repeat domain proteins: a novel target class?

“…DCAF1 is composed of an atypical kinase domain that phosphorylates nucleosomal histone 2A 85 , and a WDR domain that recruits substrate proteins to the CUL4A-RBX1-DDB1-DCAF1 E3 ubiquitin ligase complex for subsequent proteasomal degradation 86 . In human immunodeficiency virus 1 (HIV-1), the viral protein Vpr binds DCAF1 to hijack the CUL4A-RBX1-DDB1-DCAF1 complex to anti-viral proteins such as uracil DNA glycosylase (UNG), thereby aberrantly committing protective host proteins for proteasome-mediated degradation 87 . Similarly, the HIV-2 protein Vpx binds DCAF1 to usurp the CUL4A-RBX1-DDB1-DCAF1 complex for degradation of the anti-viral protein SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) 88 .…”