4GYZ | pdb_00004gyz

Mus Musculus Tdp2 Bound to dAMP and Mg2+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


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

  • 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.

    • 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.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosyl-DNA phosphodiesterase 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I
256Mus musculusMutation(s): 0 
Gene Names: Tdp2, Ttrap
EC: 3.1.4
UniProt
Find proteins for Q9JJX7 (Mus musculus)
Explore Q9JJX7 
Go to UniProtKB:  Q9JJX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JJX7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D5M
Query on D5M
Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
O [auth C]
R [auth D]
T [auth E]
J [auth A],
L [auth B],
O [auth C],
R [auth D],
T [auth E],
Y [auth H]
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
PO4
Query on PO4
Download Ideal Coordinates CCD File 
V [auth F]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL
Download Ideal Coordinates CCD File 
AA [auth I],
N [auth C],
Q [auth D]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
BA [auth I]
K [auth A]
M [auth B]
P [auth C]
S [auth D]
BA [auth I],
K [auth A],
M [auth B],
P [auth C],
S [auth D],
U [auth E],
W [auth F],
X [auth G],
Z [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.347α = 90
b = 169.326β = 90
c = 184.959γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
REFMACphasing
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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, Refinement description
  • Version 1.5: 2024-02-28
    Changes: Data collection, Database references, Derived calculations