The X-ray crystal structure of the FAM111A serine protease domain in complex with LT-C is reported, revealing the structural basis for direct inhibition of FAM111A and defining a zinc-dependent, cleavage-avoiding mechanism of protease inhibition that highlights an evolutionary arms race between SV40 and host antiviral proteases.
Abstract
SV40 Large T antigen (LT) is essential for viral replication and a key determinant of host range. This host-range function is mediated by the C-terminal domain (LT-C) through binding to the host serine protease FAM111A, but the underlying mechanism has remained unclear. Here, we report the X-ray crystal structure of the FAM111A serine protease domain in complex with LT-C, revealing the structural basis for direct inhibition of FAM111A. LT-C uses a previously unrecognized zinc-binding motif and a P1-like phenylalanine residue to engage the FAM111A active site through a substrate-mimicking mechanism while avoiding proteolytic cleavage and covalent complex formation. Mutations disrupting either feature abolish FAM111A inhibition and impair SV40 propagation in cells. Consistent with this mechanism, SV40 host restriction requires FAM111A protease activity, which must be antagonized by LT-C for productive infection. Together, these findings define a zinc-dependent, cleavage-avoiding mechanism of protease inhibition that highlights an evolutionary arms race between SV40 and host antiviral proteases.
Structural analysis reveals that ASPRV1-14 possesses distinctly hydrophobic S2/S2' pockets, dictating a strict requirement for hydrophobic residues at the P2/P2' positions of substrates and explaining its resistance to most HIV-1 PR inhibitors, except indinavir.
Xueqian Feng, Zi-Lian Chen, Chao Lan et al.· Acta Biochimica et Biophysic...· 0 citations
The tripartite motif-containing (TRIM) protein family is crucial for antiviral innate immunity. In teleost, finTRIM proteins (FTRs) represent a fish-specific TRIM subfamily that underwent extensive lineage-specific expansion. Nevertheless, the biological roles of many FTR members have yet to be fully deciphered. Here, we identified common carp finTRIM54 (CcFTR54) as potent restriction factor against spring viremia of carp virus (SVCV) infection by targeting the viral phosphoprotein (P). CcFTR54 overexpression significantly rescued the type I interferon (IFN-I) signaling from SVCV P-mediated suppression. Mechanistic investigations revealed that CcFTR54 directly bond to P protein via its PRY/SPRY domain, enhancing the recruitment of the cargo receptor NBR1 to the P protein. Consequently, NBR1 deficiency substantially attenuated both CcFTR54-mediated P protein degradation and its antiviral efficacy. Furthermore, CcFTR54 catalyzes K6- and K33-linked ubiquitination of P protein at K205, a site crucial for SVCV replication. Together, our findings unveil a novel mechanism where CcFTR54 restricts SVCV replication via NBR1-dependent selective autophagic degradation of the viral P protein, thereby broadening our insights into finTRIM-mediated antiviral immunity in teleosts.
Hongxia Gao, Fei Wang, Yihan Wang et al.· Fish and Shellfish Immunolog...· 0 citations
It is found that mutations at dimer interface residues Leu112 and Phe121 abolish recombinant Nef protein dimerization while preserving the overall Nef fold, resulting in monomeric 1:1 complexes with Hck SH3 or SH3-SH2 domain proteins.
Catherine E. Thomas, J. Alvarado, Thomas E. Smithgall· bioRxiv· 0 citations
The Hom family and canilysin are defined as helicolysins, a previously uncharacterized metzincin subfamily distinguished by a conserved Thr-turn and an accessory ND, and implicates these proteins in host-pathogen interactions, adhesion, and immunomodulation.
A. Rodríguez-Banqueri, T. Goulas, Marina Girbal-González et al.· Journal of Molecular Biology· 0 citations
Proteolytic processing is a fundamental regulatory mechanism in eukaryotic cells, yet the molecular identities and mechanisms underlying such events are often poorly defined. Silencing Defective 2 (SDE2), an essential human protein, plays important roles in mRNA splicing, DNA repair and ribosomal biogenesis. Cleavage of SDE2 downstream to its N-terminal ubiquitin-like domain (SDE2
UBL
) releases the biologically functional C-terminal domain (SDE2
CT
), highlighting the importance of this proteolytic event. However, the protease responsible for this cleavage in human cells has remained undefined. Here, we identify deubiquitinating enzyme, ubiquitin-specific protease 5 (USP5), as the selectively primary effector of SDE2 cleavage both in vitro and in cell. Biophysical and structural analysis suggests that SDE2
UBL
engages with USP5 through a two-site interaction that mirrors key features of ubiquitin recognition, supporting a mechanism of substrate mimicry. Functionally, depletion of USP5 increases intron retention in previously reported SDE2-dependent transcripts, linking the removal of SDE2
UBL
domain by USP5 to the role of SDE2 in mRNA splicing. Together, these findings reveal a non-canonical proteolytic function of USP5, uncovering a previously unrecognised regulatory axis linking deubiquitinating enzymes to protein maturation, expanding the substrate repertoire for USP5 and providing a framework for identifying protease–substrate relationships in post-translational regulation.
Liam T. Hales, Paul M. Tammiste, Adam J. Walker et al.· Nature Communications· 0 citations
APP and APLP2 Kunitz domains are identified as potent endogenous inhibitors of TMPRSS2-dependent respiratory virus infection and promising scaffolds for host-directed broad-spectrum antiviral strategies.
Jan Lawrenz, Shreyans Chatterjee, A. R. Alfonso et al.· bioRxiv· 0 citations
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