PDBsum entry 5inl

Hydrolase/DNA

PDB id: 5inl

Contents

Protein chains

255 a.a.

DNA/RNA

Ligands

EPE

PEG

Metals

_MG ×3

Waters ×721

PDB id:

5inl

Name:

Hydrolase/DNA

Title:

Mouse tdp2 reaction product (5'-phosphorylated DNA)-mg2+ complex with deoxyadenosine

Structure:

Tyrosyl-DNA phosphodiesterase 2. Chain: a, b. Fragment: unp residues 118-370. Synonym: tyr-DNA phosphodiesterase 2,5'-tyrosyl-DNA phosphodiesterase,5'-tyr-DNA phosphodiesterase,traf and tnf receptor- associated protein. Engineered: yes. DNA (5'-d(p Ap Cp Gp Ap Ap Tp Tp Cp G)-3'). Chain: c, d.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: tdp2, ttrap. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Homo sapiens. Organism_taxid: 9606

Resolution:

1.55Å R-factor: 0.131 R-free: 0.168

Authors:

M.J.Schellenberg,C.K.Vilas,R.S.Williams

Key ref:

M.J.Schellenberg et al. (2016). Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2. Nucleic Acids Res, 44, 3829-3844. PubMed id: 27060144 DOI: 10.1093/nar/gkw228

Date:

07-Mar-16 Release date: 27-Apr-16

Protein chains

Q9JJX7  (TYDP2_MOUSE) -  Tyrosyl-DNA phosphodiesterase 2 from Mus musculus

Seq: 370 a.a.

Struc: 255 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

A-C-G-A-A-T-T-C-G 9 bases

A-C-G-A-A-T-T-C-G 9 bases

Enzyme reactions

• Enzyme class: E.C.3.1.4.- - ?????

DOI no: 10.1093/nar/gkw228

Nucleic Acids Res 44:3829-3844 (2016)

PubMed id: 27060144

Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2.

M.J.Schellenberg, L.Perera, C.N.Strom, C.A.Waters, B.Monian, C.D.Appel, C.K.Vilas, J.G.Williams, D.A.Ramsden, R.S.Williams.

ABSTRACT

Mammalian Tyrosyl-DNA phosphodiesterase 2 (Tdp2) reverses Topoisomerase 2 (Top2) DNA-protein crosslinks triggered by Top2 engagement of DNA damage or poisoning by anticancer drugs. Tdp2 deficiencies are linked to neurological disease and cellular sensitivity to Top2 poisons. Herein, we report X-ray crystal structures of ligand-free Tdp2 and Tdp2-DNA complexes with alkylated and abasic DNA that unveil a dynamic Tdp2 active site lid and deep substrate binding trench well-suited for engaging the diverse DNA damage triggers of abortive Top2 reactions. Modeling of a proposed Tdp2 reaction coordinate, combined with mutagenesis and biochemical studies support a single Mg(2+)-ion mechanism assisted by a phosphotyrosyl-arginine cation-π interface. We further identify a Tdp2 active site SNP that ablates Tdp2 Mg(2+) binding and catalytic activity, impairs Tdp2 mediated NHEJ of tyrosine blocked termini, and renders cells sensitive to the anticancer agent etoposide. Collectively, our results provide a structural mechanism for Tdp2 engagement of heterogeneous DNA damage that causes Top2 poisoning, and indicate that evaluation of Tdp2 status may be an important personalized medicine biomarker informing on individual sensitivities to chemotherapeutic Top2 poisons.