4FVA

Crystal structure of truncated Caenorhabditis elegans TDP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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: https://doi.org/10.1038/nsmb.2423
  • Primary Citation of Related Structures:  
    4F1H, 4F1I, 4FPV, 4FVA, 4GEW

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-tyrosyl-DNA phosphodiesterase
A, B, C, D
256Caenorhabditis elegansMutation(s): 0 
Gene Names: Y63D3A.4
EC: 3.1.4
UniProt
Find proteins for Q9XWG3 (Caenorhabditis elegans)
Explore Q9XWG3 
Go to UniProtKB:  Q9XWG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XWG3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
AA [auth D],
G [auth A],
N [auth B],
P [auth B],
U [auth C]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
H [auth A]
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
O [auth B],
Q [auth B],
R [auth B],
S [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
T [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.6α = 90
b = 104.4β = 90.98
c = 84.7γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations