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- PDB-8yhx: Cryo-EM structure of the trimeric HerA -

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Basic information

Entry
Database: PDB / ID: 8yhx
TitleCryo-EM structure of the trimeric HerA
Components
  • DUF87 domain-containing protein
  • SIR2 family protein
KeywordsIMMUNE SYSTEM / antiphage system
Function / homologySIR2-like domain / ADENOSINE-5-DIPHOSPHORIBOSE / : / SIR2 family protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsZhen, X. / Zhou, B. / Xiong, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)321700145 China
CitationJournal: Nat Commun / Year: 2024
Title: Mechanistic basis for the allosteric activation of NADase activity in the Sir2-HerA antiphage defense system.
Authors: Xiangkai Zhen / Biao Zhou / Zihe Liu / Xurong Wang / Heyu Zhao / Shuxian Wu / Zekai Li / Jiamin Liang / Wanyue Zhang / Qingjian Zhu / Jun He / Xiaoli Xiong / Songying Ouyang /
Abstract: Sir2-HerA is a widely distributed antiphage system composed of a RecA-like ATPase (HerA) and an effector with potential NADase activity (Sir2). Sir2-HerA is believed to provide defense against phage ...Sir2-HerA is a widely distributed antiphage system composed of a RecA-like ATPase (HerA) and an effector with potential NADase activity (Sir2). Sir2-HerA is believed to provide defense against phage infection in Sir2-dependent NAD depletion to arrest the growth of infected cells. However, the detailed mechanism underlying its antiphage activity remains largely unknown. Here, we report functional investigations of Sir2-HerA from Staphylococcus aureus (SaSir2-HerA), unveiling that the NADase function of SaSir2 can be allosterically activated by the binding of SaHerA, which then assembles into a supramolecular complex with NADase activity. By combining the cryo-EM structure of SaSir2-HerA in complex with the NAD cleavage product, it is surprisingly observed that Sir2 protomers that interact with HerA are in the activated state, which is due to the opening of the α15-helix covering the active site, allowing NAD to access the catalytic pocket for hydrolysis. In brief, our study provides a comprehensive view of an allosteric activation mechanism for Sir2 NADase activity in the Sir2-HerA immune system.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF87 domain-containing protein
B: DUF87 domain-containing protein
C: DUF87 domain-containing protein
D: DUF87 domain-containing protein
E: DUF87 domain-containing protein
F: DUF87 domain-containing protein
G: SIR2 family protein
H: SIR2 family protein
I: SIR2 family protein
J: SIR2 family protein
K: SIR2 family protein
L: SIR2 family protein
M: SIR2 family protein
N: SIR2 family protein
O: SIR2 family protein
P: SIR2 family protein
Q: SIR2 family protein
R: SIR2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,003,41424
Polymers1,000,05818
Non-polymers3,3566
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
DUF87 domain-containing protein


Mass: 65255.168 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: GO782_01940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A844QRL0
#2: Protein
SIR2 family protein


Mass: 50710.613 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: GO782_01935 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1PH93
#3: Chemical
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-Em structure of the trimeric HerA / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.13_2998: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79232 / Symmetry type: POINT

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