5INO

Human Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex

• PDB DOI:  https://doi.org/10.2210/pdb5INO/pdb
• NAKB: 5INO

• Classification: hydrolase/dna
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-07 Released: 2016-04-27 
• Deposition Author(s): Schellenberg, M.J., Williams, R.S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 0.264 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

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

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

(2016) Nucleic Acids Res 44: 3829-3844

• PubMed: 27060144 
• DOI: https://doi.org/10.1093/nar/gkw228
• Primary Citation of Related Structures:  
  5HT2, 5INK, 5INL, 5INM, 5INN, 5INO, 5INP, 5INQ


• PubMed 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.

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Organizational Affiliation: 

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.19 kDa 
• Atom Count: 4,373 
• Modelled Residue Count: 519 
• Deposited Residue Count: 534 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-DNA phosphodiesterase 2	A, C [auth B]	258	Homo sapiens	Mutation(s): 0  Gene Names: TDP2, EAP2, TTRAP, AD-022 EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for O95551 (Homo sapiens) Explore O95551  Go to UniProtKB:  O95551
PHAROS:  O95551

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')	B [auth D], D [auth C]	9	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 0.264 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.663	α = 90
b = 69.663	β = 90
c = 120.677	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
DENZO	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Schellenberg, M.J., Williams, R.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1Z01ES102765

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2016-05-18
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description