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TitleA DNA phosphorothioation pathway via adenylated intermediate modulates Tdp machinery.
Journal, issue, pagesNat Chem Biol, Vol. 21, Issue 8, Page 1160-1170, Year 2025
Publish dateJan 16, 2025
AuthorsTianchen An / Qian Tan / Lixu Jiang / Li Liu / Xing Jiang / Liying Liu / Xiaofei Chang / Xihao Tian / Zixin Deng / Shuai Gao / Lianrong Wang / Shi Chen /
PubMed AbstractIn prokaryotes, the non-bridging oxygen in the DNA sugar-phosphate backbone can be enzymatically replaced by a sulfur atom, resulting in phosphorothioate (PT) modification. However, the mechanism ...In prokaryotes, the non-bridging oxygen in the DNA sugar-phosphate backbone can be enzymatically replaced by a sulfur atom, resulting in phosphorothioate (PT) modification. However, the mechanism underlying the oxygen-to-sulfur substitution remains enigmatic. In this study, we discovered a hypercompact DNA phosphorothioation system, TdpABC, in extreme thermophiles. This DNA sulfuration process occurs through two sequential steps: an initial activation step by ATP to form an adenylated intermediate, followed by a substitution step where the adenyl group is replaced with a sulfur atom. Together with the TdpA-TdpB, the TdpABC system provides anti-phage defense by degrading PT-free phage DNA. Cryogenic electron microscopy structural analysis revealed that the TdpA hexamer binds one strand of encircled duplex DNA via hydrogen bonds arranged in a spiral staircase conformation. Nevertheless, the TdpAB-DNA interaction was sensitive to the hydrophobicity of the PT sulfur. PTs inhibit ATP-driven translocation and nuclease activity of TdpAB on self-DNA, thereby preventing autoimmunity.
External linksNat Chem Biol / PubMed:39820821
MethodsEM (single particle)
Resolution2.67 - 3.1 Å
Structure data

37479

8wet

EMDB-37479, PDB-8wet:
The cryo-EM structure of TdpAB complex
Method: EM (single particle) / Resolution: 2.76 Å

37491

8wfd

EMDB-37491, PDB-8wfd:
The cryo-EM structure of TdpAB in complex with AMPPNP and DNA
Method: EM (single particle) / Resolution: 2.67 Å

38837

8y1k

EMDB-38837, PDB-8y1k:
The cryo-EM structure of TdpAB in complex with AMPPNP and PT-DNA
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

Source
  • thermus antranikianii dsm 12462 (bacteria)
KeywordsTRANSLOCASE / DNA phosphorothioation / antiphage / nuclease / TRANSLOCASE/DNA / TRANSLOCASE-DNA complex

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