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 1.1 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:  
    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 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
MoleculeChainsSequence LengthOrganismDetailsImage
5'-tyrosyl-DNA phosphodiesteraseA, B, C, D256Caenorhabditis 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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