4F1H

Crystal structure of TDP2 from Danio rerio complexed with a single strand DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.662 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.

Shi, K.Kurahashi, K.Gao, R.Tsutakawa, S.E.Tainer, J.A.Pommier, Y.Aihara, H.

(2012) Nat.Struct.Mol.Biol. 19: 1372-1377

  • DOI: 10.1038/nsmb.2423
  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-DNA phosphodiesterase 2
A
250Danio rerioMutation(s): 0 
Gene Names: tdp2 (ttrap, ttrapl)
EC: 3.1.4.-
Find proteins for Q5XJA0 (Danio rerio)
Go to UniProtKB:  Q5XJA0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-DNA phosphodiesterase 2
B
251Danio rerioMutation(s): 0 
Gene Names: tdp2 (ttrap, ttrapl)
EC: 3.1.4.-
Find proteins for Q5XJA0 (Danio rerio)
Go to UniProtKB:  Q5XJA0
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*CP*AP*G)-3')C5N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.662 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.918α = 90.00
b = 95.100β = 90.00
c = 104.732γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references