4F1I

Crystal structure of SeMet TDP2 from Caenorhabditis elegans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 1
MoleculeChainsSequence LengthOrganismDetails
5'-tyrosyl-DNA phosphodiesterase
A
362Caenorhabditis elegansMutation(s): 0 
EC: 3.1.4.-
Find proteins for Q9XWG3 (Caenorhabditis elegans)
Go to UniProtKB:  Q9XWG3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.685α = 90.00
b = 100.685β = 90.00
c = 121.375γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata scaling
Blu-Icedata collection
PHENIXphasing
PHENIXmodel building
d*TREKdata reduction

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
  • Version 1.2: 2017-11-15
    Type: Refinement description