4GZ0 | pdb_00004gz0

Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex

• PDB DOI: https://doi.org/10.2210/pdb4GZ0/pdb
• NAKB: 4GZ0

• Classification: HYDROLASE/dna
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-05 Released: 2012-10-31 
• Deposition Author(s): Schellenberg, M.J., Williams, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.

Schellenberg, M.J., Appel, C.D., Adhikari, S., Robertson, P.D., Ramsden, D.A., Williams, R.S.

(2012) Nat Struct Mol Biol 19: 1363-1371

• PubMed: 23104055 
• DOI: https://doi.org/10.1038/nsmb.2418
• Primary Citation of Related Structures:  
  4GYZ, 4GZ0, 4GZ1, 4GZ2


• PubMed Abstract: 
  

  The topoisomerase II (topo II) DNA incision-and-ligation cycle can be poisoned (for example following treatment with cancer chemotherapeutics) to generate cytotoxic DNA double-strand breaks (DSBs) with topo II covalently conjugated to DNA. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) protects genomic integrity by reversing 5'-phosphotyrosyl-linked topo II-DNA adducts. Here, X-ray structures of mouse Tdp2-DNA complexes reveal that Tdp2 β-2-helix-β DNA damage-binding 'grasp', helical 'cap' and DNA lesion-binding elements fuse to form an elongated protein-DNA conjugate substrate-interaction groove. The Tdp2 DNA-binding surface is highly tailored for engagement of 5'-adducted single-stranded DNA ends and restricts nonspecific endonucleolytic or exonucleolytic processing. Structural, mutational and functional analyses support a single-metal ion catalytic mechanism for the exonuclease-endonuclease-phosphatase (EEP) nuclease superfamily and establish a molecular framework for targeted small-molecule blockade of Tdp2-mediated resistance to anticancer topoisomerase drugs.

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Organizational Affiliation: 
• Laboratory of Structural Biology, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, North Carolina, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 198.65 kDa 
• Atom Count: 14,788 
• Modeled Residue Count: 1,552 
• Deposited Residue Count: 1,590 
• 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, B, E, G [auth K], I [auth G], K [auth I]	256	Mus musculus	Mutation(s): 0  Gene Names: Tdp2, Ttrap EC: 3.1.4
UniProt
Find proteins for Q9JJX7 (Mus musculus) Explore Q9JJX7  Go to UniProtKB:  Q9JJX7

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')	C, D, F, H [auth L], J [auth H], L [auth J]	9	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6AH	ID [auth L], MB [auth C], NB [auth D], PC [auth F], VE [auth J], XD [auth H]	6-aminohexan-1-ol C6 H15 N O SUTWPJHCRAITLU-UHFFFAOYSA-N
EDO	AA [auth A], AB [auth B], AC [auth E], AD [auth K], AE [auth H], BA [auth A], BB [auth B], BC [auth E], BD [auth K], BE [auth I], CA [auth A], CB [auth B], CC [auth E], CD [auth K], CE [auth I], DA [auth A], DB [auth B], DC [auth E], DD [auth K], DE [auth I], EA [auth A], EB [auth B], EC [auth E], ED [auth K], EE [auth I], FA [auth A], FB [auth B], FC [auth E], FE [auth I], GA [auth A], GB [auth B], GC [auth E], GE [auth I], HA [auth A], HB [auth B], HC [auth E], HE [auth I], IB [auth B], IC [auth E], IE [auth I], JC [auth E], JD [auth G], JE [auth I], KC [auth E], KD [auth G], KE [auth I], LD [auth G], LE [auth I], M [auth A], MD [auth G], ME [auth I], N [auth A], NA [auth B], ND [auth G], NE [auth I], O [auth A], OA [auth B], OB [auth D], OD [auth G], OE [auth I], P [auth A], PA [auth B], PB [auth D], PD [auth G], PE [auth I], Q [auth A], QA [auth B], QB [auth D], QC [auth F], QD [auth G], QE [auth I], R [auth A], RA [auth B], RB [auth E], RC [auth K], RD [auth G], S [auth A], SA [auth B], SB [auth E], SC [auth K], SD [auth G], T [auth A], TA [auth B], TB [auth E], TC [auth K], TD [auth G], U [auth A], UA [auth B], UB [auth E], UC [auth K], V [auth A], VA [auth B], VB [auth E], VC [auth K], W [auth A], WA [auth B], WB [auth E], WC [auth K], WE [auth J], X [auth A], XA [auth B], XB [auth E], XC [auth K], Y [auth A], YA [auth B], YB [auth E], YC [auth K], YD [auth H], Z [auth A], ZA [auth B], ZB [auth E], ZC [auth K], ZD [auth H]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	FD [auth K], GD [auth K], HD [auth K], IA [auth A], JA [auth A], JB [auth B], KA [auth A], KB [auth B], LA [auth A], LB [auth B], LC [auth E], MA [auth A], MC [auth E], NC [auth E], OC [auth E], RE [auth I], SE [auth I], TE [auth I], UD [auth G], UE [auth I], VD [auth G], WD [auth G]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.9	α = 90
b = 121.1	β = 90
c = 167.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
PHASER	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Schellenberg, M.J., Williams, R.S.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references
• Version 1.2: 2012-11-28
  Changes: Database references
• Version 1.3: 2013-01-02
  Changes: Database references
• Version 1.4: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2024-02-28
  Changes: Data collection, Database references, Derived calculations