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Updated: May 17, 2026
Nuclear Magnetic Resonance Spectroscopy for the Identification of Multiple Phosphorylations of Intrinsically Disordered Proteins
Published on: December 27, 2016
Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2
Ke Shi1, Kayo Kurahashi, Rui Gao
1Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.
Abstract:
The DNA-repair enzyme Tdp2 resolves 5'-phosphotyrosyl DNA adducts and mediates resistance to anticancer drugs that target covalent topoisomerase-DNA complexes. Tdp2 also participates in key signaling pathways during development and tumorigenesis and cleaves a protein-RNA linkage during picornavirus replication. The crystal structure of zebrafish Tdp2 bound to DNA reveals a deep, narrow basic groove that selectively accommodates the 5' end of single-stranded DNA in a stretched conformation. The crystal structure of the full-length Caenorhabditis elegans Tdp2 shows that this groove can also accommodate an acidic peptide stretch in vitro, with glutamate and aspartate side chains occupying the DNA backbone phosphate-binding sites. This extensive molecular mimicry suggests a potential mechanism for autoregulation and interaction of Tdp2 with phosphorylated proteins in signaling. Our study provides a framework to interrogate functions of Tdp2 and develop inhibitors for chemotherapeutic and antiviral applications.
Insights
The DNA-repair enzyme Tdp2 resolves DNA adducts and aids anticancer drug resistance. Its structure reveals a groove that binds DNA and mimics protein interactions, suggesting roles in signaling and autoregulation.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Tdp2 (tyrosyl-DNA phosphodiesterase 2) is a DNA-repair enzyme crucial for resolving 5'-phosphotyrosyl DNA adducts.
- It confers resistance to anticancer drugs targeting topoisomerase-DNA complexes.
- Tdp2 plays roles in developmental signaling, tumorigenesis, and viral RNA processing.
Purpose of the Study:
- To elucidate the structural basis of Tdp2's DNA binding and catalytic mechanism.
- To investigate Tdp2's potential interactions with protein substrates through structural mimicry.
- To provide a foundation for developing Tdp2-targeted therapeutics.
Main Methods:
- X-ray crystallography of zebrafish Tdp2 bound to DNA.
- X-ray crystallography of full-length Caenorhabditis elegans Tdp2.
- Structural analysis of DNA-binding groove and peptide interactions.
Main Results:
- Crystal structure of zebrafish Tdp2 reveals a basic groove accommodating single-stranded DNA.
- Crystal structure of C. elegans Tdp2 shows the groove binding acidic peptide stretches.
- Identified molecular mimicry between DNA binding and potential protein interactions.
Conclusions:
- The Tdp2 active site groove exhibits remarkable plasticity, accommodating both DNA and peptide substrates.
- Molecular mimicry suggests a mechanism for Tdp2 autoregulation and interaction with phosphorylated signaling proteins.
- Structural insights pave the way for designing Tdp2 inhibitors for cancer and viral diseases.
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