Direct recognition of viral proteins is key to bacterial immunity. Here, Evans et al. uncover the mechanisms used by two distinct defense proteins to detect the phage DNA packaging motor mechanisms: b...

Prokaryotes employ diverse defense strategies to detect and halt the progression of phage infection. Multiple defense systems sense phage proteins through direct binding, including antiviral STAND NTPases (Avs), which oligomerize upon target recognition to induce programmed cell death. The widespread Avs2 family was previously shown to detect the large terminase subunit of tailed phages, but the mechanism of terminase sensing was unknown. Here, we determine the structural basis of terminase recognition by Avs2 from Escherichia coli (EcAvs2). A cryo-EM structure at 2.3 Å resolution reveals that EcAvs2 forms a flat, C4-symmetric tetramer in which each protomer is bound to a single terminase monomer. Terminase recognition is mediated by a large, shape complementary binding pocket in the EcAvs2 sensor domain, including specific contacts with an unexpected ATP molecule at the interface of EcAvs2 and terminase. Furthermore, we demonstrate that the defense protein Upx also recognizes diverse phage terminases, despite lacking sequence and structural homology to Avs. AlphaFold 3 models indicate that Upx binds an unfolded state of the core terminase ATPase domain, mediated by β-augmentation. These findings highlight the distinct modes of terminase recognition across structurally diverse defense proteins. ### Competing Interest Statement F.Z. is a scientific advisor and cofounder of Beam Therapeutics, Pairwise Plants, Arbor Biotechnologies, Aera Therapeutics, and Moonwalk Biosciences. F.Z. is a scientific advisor for Octant. The remaining authors have no competing interests to declare. National Institute of General Medical Sciences, 5T32GM007276, 5T32GM141828 Stanford Bio-X Helen Hay Whitney Foundation, https://ror.org/037ebw447 Howard Hughes Medical Institute, https://ror.org/006w34k90 Yang Tan Collective K. Lisa Yang and Hock E. Tan Molecular Therapeutics Center Broad Institute Programmable Therapeutics Donors BT Charitable Foundation G. Harold & Leila Y. Mathers Foundation, MF-2303-04116 Stanford University School of Medicine, https://ror.org/011pcwc98

A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.

Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...

The eukaryotic vault particle is a giant ribonucleoprotein complex that assembles into an iconic barrel-like cage. Its cellular function has remained elusive despite extensive characterization. Using ...

Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...

Martinkus et al. show that Photorhabdus and Xenorhabdus species encode arrays of immunity genes whose protein products neutralize toxins secreted by competitors. These arrays, often linked to Xer pass...

From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...

We discover and study reverse transcriptases

Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...

Linked protease–effector modules are widespread in prokaryotic antiviral defense, yet the mechanisms of most remain poorly understood. Here we show that four of the most prevalent modules—metallo-β-la...