4PE8

Crystal structure of TatD in complex with trinucleotide DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

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This is version 1.3 of the entry. See complete history


Literature

Structure and function of TatD exonuclease in DNA repair.

Chen, Y.C.Li, C.L.Hsiao, Y.Y.Duh, Y.Yuan, H.S.

(2014) Nucleic Acids Res 42: 10776-10785

  • DOI: 10.1093/nar/gku732
  • Primary Citation of Related Structures:  
    2LUN, 4P5U, 4PE8

  • PubMed Abstract: 
  • TatD is an evolutionarily conserved protein with thousands of homologues in all kingdoms of life. It has been suggested that TatD participates in DNA fragmentation during apoptosis in eukaryotic cells. However, the cellular functions and biochemical properties of TatD in bacterial and non-apoptotic eukaryotic cells remain elusive ...

    TatD is an evolutionarily conserved protein with thousands of homologues in all kingdoms of life. It has been suggested that TatD participates in DNA fragmentation during apoptosis in eukaryotic cells. However, the cellular functions and biochemical properties of TatD in bacterial and non-apoptotic eukaryotic cells remain elusive. Here we show that Escherichia coli TatD is a Mg(2+)-dependent 3'-5' exonuclease that prefers to digest single-stranded DNA and RNA. TatD-knockout cells are less resistant to the DNA damaging agent hydrogen peroxide, and TatD can remove damaged deaminated nucleotides from a DNA chain, suggesting that it may play a role in the H2O2-induced DNA repair. The crystal structure of the apo-form TatD and TatD bound to a single-stranded three-nucleotide DNA was determined by X-ray diffraction methods at a resolution of 2.0 and 2.9 Å, respectively. TatD has a TIM-barrel fold and the single-stranded DNA is bound at the loop region on the top of the barrel. Mutational studies further identify important conserved metal ion-binding and catalytic residues in the TatD active site for DNA hydrolysis. We thus conclude that TatD is a new class of TIM-barrel 3'-5' exonuclease that not only degrades chromosomal DNA during apoptosis but also processes single-stranded DNA during DNA repair.


    Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROC Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10048, Taiwan, ROC hanna@sinica.edu.tw.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tat-linked quality control protein TatDA260Escherichia coli K-12Mutation(s): 0 
Gene Names: tatDmttCyigWyigXb4483JW5931
EC: 3.1.15 (PDB Primary Data), 3.1.11 (UniProt), 3.1.13 (UniProt)
UniProt
Find proteins for P27859 (Escherichia coli (strain K12))
Explore P27859 
Go to UniProtKB:  P27859
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27859
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*T)-3')B3synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.45α = 90
b = 52.871β = 90
c = 101.107γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
Cootmodel building
PDB_EXTRACTdata extraction
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-04-17
    Changes: Author supporting evidence, Data collection