Structure of a human DNA repair protein UBA domain that interacts with HIV-1 Vpr

Abstract

The HIV-1 protein Vpr is critical for a number of viral functions including a unique ability to arrest T-cells at a G2/M checkpoint and induce subsequent apoptosis. It has been shown to interact specifically with the second UBA (ubiquitin associated) domain found in the DNA repair protein HHR23A, a highly evolutionarily conserved protein. This domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. The three dimensional structure of the UBA domain, determined by NMR spectroscopy, is presented. The protein domain forms a compact three-helix bundle. One side of the protein has a hydrophobic surface that is the most likely Vpr target site.

Cbl-b interacts with ubiquitinated proteins; differential functions of the UBA domains of c-Cbl and Cbl-b

“…The UBA and CUE domains have both been demonstrated to interact with ubiquitin via a hydrophobic patch (Hofmann and Bucher, 1996;Dieckmann et al, 1998;Withers-Ward et al, 2000;Mueller and Feigon, 2002;Ciani et al, 2003;Kang et al, 2003;Prag et al, 2003;Ryu et al, 2003;Wang et al, 2003;Mueller et al, 2004;Yuan et al, 2004). Molecular modeling of the UBA b and the UBA c suggests that the hydrophobic surfaces of these domains are similar to each other ( Figure 4b).…”

“…Like the UBA b , the UBA domains of Rad23a, UBA(1) and UBA(2), bind ubiquitin (Bertolaet et al, 2001a;Chen et al, 2001;Wilkinson et al, 2001;Rao and Sastry, 2002;Raasi and Pickart, 2003;Ryu et al, 2003). While they have a similar structure (Hofmann and Bucher, 1996;Dieckmann et al, 1998;Withers-Ward et al, 2000;Mueller and Feigon, 2002;Ryu et al, 2003), there is very little sequence homology between these UBA domains ( Figure 4a). For example, the two HsRad23a UBA domains have 49% similarity.…”

“…Since the interaction between UBA domains and ubiquitin are mediated by a hydrophobic patch on the surface of the UBA domain (Hofmann and Bucher, 1996;Dieckmann et al, 1998;Withers-Ward et al, 2000;Mueller and Feigon, 2002;Ciani et al, 2003;Kang et al, 2003;Prag et al, 2003;Ryu et al, 2003;Wang et al, 2003;Mueller et al, 2004;Yuan et al, 2004), we compared this area in the Cbl UBA domains. We modeled the UBA b and the UBA c on the solution structure of the UBA(1) of HsRad23 using GeneFold (Jaroszewski et al, 1998) (SYBYL, version 6.8; Tripos, Inc., St Louis, MO, USA) and SWISSMODEL (Schwede et al, 2003).…”

“…The structures of the UBA domains of HsRad23a (Hofmann and Bucher, 1996;Dieckmann et al, 1998;Withers-Ward et al, 2000;Mueller and Feigon, 2002;Ryu et al, 2003), p62 (Ciani et al, 2003), p47 (Yuan et al, 2004), and Swa2p (Chim et al, 2004) have been described recently. Like the closely related CUE domain, the UBA domain is a tightly packed threehelix bundle with a hydrophobic surface that mediates the interaction with ubiquitin (Hofmann and Bucher, 1996;Dieckmann et al, 1998;Withers-Ward et al, 2000;Mueller and Feigon, 2002;Ciani et al, 2003;Kang et al, 2003;Prag et al, 2003;Ryu et al, 2003;Wang et al, 2003;Chim et al, 2004;Mueller et al, 2004;Yuan et al, 2004).…”

Solution Conformation of Lys63-linked Di-ubiquitin Chain Provides Clues to Functional Diversity of Polyubiquitin Signaling

“…The UBA construct used in this study contains a full-length UBA2 domain from HHR23A (human isoform A of Rad23), residues 315-363 in the protein sequence (SWS P54725). These residues are numbered here Ϫ3 through 45 to bring residues 1-45 in correspondence to those in the PDB structure 1DV0 (24). In addition, this construct has a 5-residue N-terminal extension (GSAAA) resulting from the fusion junction.…”