6MDX

Mechanism of protease dependent DPC repair

Summary for 6MDX

• Entry DOI: 10.2210/pdb6mdx/pdb
• Descriptor: SprT-like domain-containing protein Spartan, DNA (5'-D(P*CP*C)-3'), 1,2-ETHANEDIOL, ... (7 entities in total)
• Functional Keywords: dpc repair, protease, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 23128.98

Authors

Li, F.,Raczynska, J.,Chen, Z.,Yu, H. (deposition date: 2018-09-05, release date: 2019-04-10, Last modification date: 2025-04-02)

Primary citation

Li, F.,Raczynska, J.E.,Chen, Z.,Yu, H.
Structural Insight into DNA-Dependent Activation of Human Metalloprotease Spartan.
Cell Rep, 26:3336-3346.e4, 2019

PubMed Abstract: The DNA-dependent metalloprotease Spartan (SPRTN) cleaves DNA-protein crosslinks (DPCs) and protects cells from DPC-induced genome instability. Germline mutations of SPRTN are linked to human Ruijs-Aalfs syndrome (RJALS) characterized by progeria and early-onset hepatocellular carcinoma. The mechanism of DNA-mediated activation of SPRTN is not understood. Here, we report the crystal structure of the human SPRTN SprT domain bound to single-stranded DNA (ssDNA). Our structure reveals a Zn-binding sub-domain (ZBD) in SprT that shields its active site located in the metalloprotease sub-domain (MPD). The narrow catalytic groove between MPD and ZBD only permits cleavage of flexible substrates. The ZBD contains an ssDNA-binding site, with a DNA-base-binding pocket formed by aromatic residues. Mutations of ssDNA-binding residues diminish the protease activity of SPRTN. We propose that the ZBD contributes to the ssDNA specificity of SPRTN, restricts the access of globular substrates, and positions DPCs, which may need to be partially unfolded, for optimal cleavage.

PubMed: 30893605
DOI: 10.1016/j.celrep.2019.02.082

Experimental method

X-RAY DIFFRACTION (1.55 Å)