8BTO | pdb_00008bto

Helical structure of BcThsA in complex with 1''-3'gcADPR

PDB DOI: https://doi.org/10.2210/pdb8BTO/pdb
EM Map EMD-16233: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Bacillus cereus MSX-D12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-11-29 Released: 2024-02-21
Deposition Author(s): Tamulaitiene, G., Sasnauskas, G., Sabonis, D.
Funding Organization(s): Research Council of Lithuania

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Activation of Thoeris antiviral system via SIR2 effector filament assembly.

Tamulaitiene, G., Sabonis, D., Sasnauskas, G., Ruksenaite, A., Silanskas, A., Avraham, C., Ofir, G., Sorek, R., Zaremba, M., Siksnys, V.

(2024) Nature 627: 431-436

PubMed: 38383786 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-024-07092-x
Primary Citation Related Structures:
8BTN, 8BTO, 8BTP

PubMed Abstract:
To survive bacteriophage (phage) infections, bacteria developed numerous anti-phage defence systems ^1-7. Some of them (for example, type III CRISPR-Cas, CBASS, Pycsar and Thoeris) consist of two modules: a sensor responsible for infection recognition and an effector that stops viral replication by destroying key cellular components ^8-12. In the Thoeris system, a Toll/interleukin-1 receptor (TIR)-domain protein, ThsB, acts as a sensor that synthesizes an isomer of cyclic ADP ribose, 1''-3' glycocyclic ADP ribose (gcADPR), which is bound in the Smf/DprA-LOG (SLOG) domain of the ThsA effector and activates the silent information regulator 2 (SIR2)-domain-mediated hydrolysis of a key cell metabolite, NAD ⁺ (refs. ^12-14). Although the structure of ThsA has been solved ¹⁵, the ThsA activation mechanism remained incompletely understood. Here we show that 1''-3' gcADPR, synthesized in vitro by the dimeric ThsB' protein, binds to the ThsA SLOG domain, thereby activating ThsA by triggering helical filament assembly of ThsA tetramers. The cryogenic electron microscopy (cryo-EM) structure of activated ThsA revealed that filament assembly stabilizes the active conformation of the ThsA SIR2 domain, enabling rapid NAD ⁺ depletion. Furthermore, we demonstrate that filament formation enables a switch-like response of ThsA to the 1''-3' gcADPR signal.

Organizational Affiliation

Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania. giedre.tamulaitiene@bti.vu.lt.

Macromolecule Content

Total Structure Weight: 679.47 kDa
Atom Count: 46,128
Modeled Residue Count: 5,676
Deposited Residue Count: 5,748
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(+) hydrolase ThsA	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	479	Bacillus cereus MSX-D12	Mutation(s): 1 Gene Names: thsA, II9_05448 EC: 3.2.2.5
UniProt
Find proteins for J8G6Z1 (Bacillus cereus (strain MSX-D12)) Explore J8G6Z1 Go to UniProtKB: J8G6Z1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J8G6Z1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain V [auth E] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain N [auth A] SDF format, chain JA [auth L] SDF format, chain HA [auth K] SDF format, chain FA [auth J] SDF format, chain DA [auth I] SDF format, chain BA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain V [auth E] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth A] MOL2 format, chain JA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain BA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain V [auth E] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth A] mmCIF format, chain JA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain BA [auth H]	BA [auth H] DA [auth I] FA [auth J] HA [auth K] JA [auth L] BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]
OJC (Subject of Investigation/LOI) Query on OJC Download:Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain IA [auth L] SDF format, chain GA [auth K] SDF format, chain EA [auth J] SDF format, chain CA [auth I] SDF format, chain AA [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth L] MOL2 format, chain GA [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain AA [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth L] mmCIF format, chain GA [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth I] EA [auth J] GA [auth K] IA [auth L] AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	(2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione C₁₅ H₂₁ N₅ O₁₃ P₂ NDSLKXAJVDJCEG-ZQSHOCFMSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]