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Structure paper

TitleTIR-like NADases act in bacterial immunity and the RNA vault.
Journal, issue, pagesbioRxiv, Year 2026
Publish dateMay 5, 2026
AuthorsAdam Osinski / Benjamin Mayro / Victor A Lopez / Jason Schrad / Hannah Choi / Diana R Tomchick / Krzysztof Pawłowski / Kevin Forsberg / Sarah H Shahmoradian / Vincent S Tagliabracci
PubMed AbstractAcross all domains of life, organisms exploit NAD metabolism as a central line of defense against invading pathogens. Here, we show that domain of unknown function 4062 (DUF4062) is a widespread ...Across all domains of life, organisms exploit NAD metabolism as a central line of defense against invading pathogens. Here, we show that domain of unknown function 4062 (DUF4062) is a widespread family of TIR-like NADases that hydrolyze NAD to ADP-ribose and nicotinamide. In bacteria, DUF4062 homologs form a previously unrecognized antiphage defense system, which we name Swarożyc, that assembles with the phage portal into a supramolecular NADase complex to induce abortive infection. In eukaryotes, DUF4062 is found in TEP1, which we demonstrate functions as an active NADase within the RNA vault, an enigmatic organelle-like structure. Single-particle cryo-electron microscopy reveals ADP-ribose bound within the shoulder of both reconstituted and human brain vaults, while cryo-electron tomography positions TEP1 along the central axis at the shoulder. Thus, TEP1, like bacterial Swarożyc, functions by depleting NAD , providing new insight into the long-standing mystery of vault function.
External linksbioRxiv / PubMed:42146377 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.87 - 2.85 Å
Structure data

75498

10wc

EMDB-75498, PDB-10wc:
KpSwz DUF4062 (Hexamer, catalytic mutant E97A)
Method: EM (single particle) / Resolution: 2.42 Å

75622

11cq

EMDB-75622, PDB-11cq:
KpSwz in complex with bacteriophage Bas14 Portal
Method: EM (single particle) / Resolution: 2.53 Å

75626

11cv

EMDB-75626, PDB-11cv:
KpSwz DUF4062 (Tetramer, catalytic mutant E97A)
Method: EM (single particle) / Resolution: 2.66 Å

75638

11dr

EMDB-75638, PDB-11dr:
Human Brain RNA Vault Shoulder bound to ADPR, focused refinement (EMPIAR-10766)
Method: EM (single particle) / Resolution: 2.62 Å

75642

11dv

EMDB-75642, PDB-11dv:
RNA Vault waist region, focused refinement (MVP/TEP1 sample)
Method: EM (single particle) / Resolution: 2.33 Å

75647

11ee

EMDB-75647, PDB-11ee:
RNA Vault shoulder region with BAD bound, focused refinement (MVP/TEP1 sample)
Method: EM (single particle) / Resolution: 1.87 Å

75656

11eq

EMDB-75656, PDB-11eq:
RNA Vault with BAD bound (MVP/TEP1 sample)
Method: EM (single particle) / Resolution: 2.17 Å

75664

11fh

EMDB-75664, PDB-11fh:
RNA Vault cap (MVP/PARP4/TEP1 sample)
Method: EM (single particle) / Resolution: 1.92 Å

75731

11jb

EMDB-75731, PDB-11jb:
RNA Vault with ADPR bound (MVP/PARP4/TEP1 NADP sample)
Method: EM (single particle) / Resolution: 2.16 Å

75732

11jc

EMDB-75732, PDB-11jc:
RNA Vault Shoulder with ADPR bound, compact conformation, focused refinement (MVP/PARP4/TEP1 NADP sample)
Method: EM (single particle) / Resolution: 1.96 Å

75733

11jd

EMDB-75733, PDB-11jd:
RNA Vault Shoulder with ADPR bound, extended conformation, focused refinement (MVP/PARP4/TEP1 NADP sample)
Method: EM (single particle) / Resolution: 2.37 Å

75735

11jf

EMDB-75735, PDB-11jf:
RNA Vault bound to PARP4 MINT, focused refinement (MVP/PARP4/TEP1 NADP sample)
Method: EM (single particle) / Resolution: 2.85 Å

EMDB-75744: RNA Vault intermediate conformation (MVP/PARP4/TEP1 sample)
Method: EM (single particle) / Resolution: 2.67 Å

EMDB-75745: RNA Vault extended conformation (MVP/PARP4/TEP1 sample)
Method: EM (single particle) / Resolution: 2.24 Å

PDB-11gz:
TEP1 TIR/DUF4062 domain
Method: X-RAY DIFFRACTION / Resolution: 2.44 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-MG:
Unknown entry

ChemComp-AR6:
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL

ChemComp-DQV:
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-SO4:
SULFATE ION

Source
  • klebsiella pneumoniae (bacteria)
  • escherichia phage theodorherzl (virus)
  • homo sapiens (human)
KeywordsHYDROLASE / DUF4062 / TIR / Anti-phage defense / bacterial immunity / NADase / Bacteriophage / phage / portal protein / TIR domain / STRUCTURAL PROTEIN / RNA Vault / ADPR / ADP-ribose / Nucleotide / Major Vault Protein / BAD / benzamide adenine dinucleotide / NAD-ase / TEP1 / complex / PARP4

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