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Structure paper

TitleAssembly-mediated activation of the SIR2-HerA supramolecular complex for anti-phage defense.
Journal, issue, pagesMol Cell, Vol. 83, Issue 24, Page 4586-44599.e5, Year 2023
Publish dateDec 21, 2023
AuthorsZhangfei Shen / Qingpeng Lin / Xiao-Yuan Yang / Elizabeth Fosuah / Tian-Min Fu /
PubMed AbstractSIR2-HerA, a bacterial two-protein anti-phage defense system, induces bacterial death by depleting NAD upon phage infection. Biochemical reconstitution of SIR2, HerA, and the SIR2-HerA complex ...SIR2-HerA, a bacterial two-protein anti-phage defense system, induces bacterial death by depleting NAD upon phage infection. Biochemical reconstitution of SIR2, HerA, and the SIR2-HerA complex reveals a dynamic assembly process. Unlike other ATPases, HerA can form various oligomers, ranging from dimers to nonamers. When assembled with SIR2, HerA forms a hexamer and converts SIR2 from a nuclease to an NAD hydrolase, representing an unexpected regulatory mechanism mediated by protein assembly. Furthermore, high concentrations of ATP can inhibit NAD hydrolysis by the SIR2-HerA complex. Cryo-EM structures of the SIR2-HerA complex reveal a giant supramolecular assembly up to 1 MDa, with SIR2 as a dodecamer and HerA as a hexamer, crucial for anti-phage defense. Unexpectedly, the HerA hexamer resembles a spiral staircase and exhibits helicase activities toward dual-forked DNA. Together, we reveal the supramolecular assembly of SIR2-HerA as a unique mechanism for switching enzymatic activities and bolstering anti-phage defense strategies.
External linksMol Cell / PubMed:38096827
MethodsEM (single particle)
Resolution2.83 - 3.6 Å
Structure data

40762

8su9

EMDB-40762, PDB-8su9:
E. coli SIR2-HerA complex (hexamer HerA bound with dodecamer Sir2)
Method: EM (single particle) / Resolution: 2.83 Å

40763

8sub

EMDB-40763, PDB-8sub:
E. coli SIR2-HerA complex (dodecamer SIR2 pentamer HerA)
Method: EM (single particle) / Resolution: 2.89 Å

40778

8suw

EMDB-40778, PDB-8suw:
E. coli SIR2-HerA complex (dodecamer SIR2 bound 4 protomers of HerA)
Method: EM (single particle) / Resolution: 3.15 Å

40860

8sxx

EMDB-40860, PDB-8sxx:
E. coli dodecamer SIR2
Method: EM (single particle) / Resolution: 3.6 Å

42061

8uae

EMDB-42061, PDB-8uae:
E. coli Sir2_HerA complex (12:6) with ATPgamaS
Method: EM (single particle) / Resolution: 3.25 Å

42062

8uaf

EMDB-42062, PDB-8uaf:
E. coli Sir2_HerA complex (12:6) bound with NAD+
Method: EM (single particle) / Resolution: 3.18 Å

Chemicals

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

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-MG:
Unknown entry

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

Source
  • escherichia coli (E. coli)
KeywordsIMMUNE SYSTEM / HerA / SIR2 / NADase / ATPase / Anti-phage system / Anti-phage / Nuclease

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