Molecular basis of the interaction of the human tyrosine phosphatase PTPN3 with the hepatitis B virus core protein

Abstract

Interactions between the hepatitis B virus core protein (HBc) and host cell proteins are poorly understood, although they may be essential for the propagation of the virus and its pathogenicity. HBc has a C-terminal PDZ (PSD-95, Dlg1, ZO-1)-binding motif (PBM) that is responsible for interactions with host PDZ domain-containing proteins. In this work, we focused on the human protein tyrosine phosphatase non-receptor type 3 (PTPN3) and its interaction with HBc. We solved the crystal structure of the PDZ domain of PTPN3 in complex with the PBM of HBc, revealing a network of interactions specific to class I PDZ domains despite the presence of a C-terminal cysteine in this atypical PBM. We further showed that PTPN3 binds the HBc protein within capsids or as a homodimer. We demonstrate that overexpression of PTPN3 significantly affects HBV infection in HepG2 NTCP cells. Finally, we performed proteomics studies on both sides by pull-down assays and screening of a human PDZ domain library. We identified a pool of human PBM-containing proteins that might interact with PTPN3 in cells and that could be in competition with the HBc PBM during infection, and we also identified potential cellular partners of HBc through PDZ-PBM interactions. This study opens up many avenues of future investigations into the pathophysiology of HBV.

A Thermodynamic Analysis of the Binding Specificity between Four Human PDZ Domains and Eight Host, Viral and Designed Ligands

“…In addition, two of the three viral ligands interact with nNOS-PDZ, which has not been described to be the target of any virus up to date. Our results agree with previous high-throughput studies that report the interaction of individual viral proteins with up to dozens of host PDZ domains [63][64][65][66][67][68]. It may be the case that viruses have evolved to sequester a diverse range of host PDZ partners, exploiting the intrinsic interaction plasticity of the PDZ fold [69].…”

Quantitative fragmentomics allow affinity mapping of interactomes

“…Most LYSC data originate from previous articles 19 – 22 , 26 , 68 , 69 . Additional LYSC holdup experiments were carried out as previously described, using only the original layout.…”

Host PDZ‐containing proteins targeted by SARS‐CoV‐2

“…These proteins have not been identified as binders of proteins E and 3a. GIPC1 is a PDZ‐containing protein recognized by the PBM of the hepatitis B virus capsid protein and can accommodate another atypical small C‐terminal residue, a cysteine [25].…”

“…The affinity‐based ranking of the identified binders of E protein provided a specificity profile. As comparison, the class I PBMs of NS5 protein from West Nile virus (WNV) and of capsid protein from hepatitis B virus interact with 29 and 28 PDZ binders [25,28], respectively, while about 50 PDZ proteins bind to the class I PBM of E6 viral oncoprotein from HPV16 [19]. By contrast, class II PBMs generally display lower affinities for their target and consequently a lowest number of binders in comparison with the class I PBMs.…”