4P5U | pdb_00004p5u

Crystal structure of TatD

• PDB DOI: https://doi.org/10.2210/pdb4P5U/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-20 Released: 2014-08-27 
• Deposition Author(s): Chen, Y., Li, C.-L., Hsiao, Y.-Y., Duh, Y., Yuan, H.S.
• Funding Organization(s): Ministry of Science and Technology (Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

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

• PubMed: 25114049 
• DOI: https://doi.org/10.1093/nar/gku732
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROC.
Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan, ROC.
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 [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.25 kDa 
• Atom Count: 2,273 
• Modeled Residue Count: 262 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tat-linked quality control protein TatD	A	262	Escherichia coli K-12	Mutation(s): 0  Gene Names: tatD, mttC, yigW, yigX, b4483, JW5931 EC: 3.1.15 (PDB Primary Data), 3.1.13 (UniProt), 3.1.11 (UniProt)
UniProt
Find proteins for P27859 (Escherichia coli (strain K12)) Explore P27859  Go to UniProtKB:  P27859

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.165	α = 90
b = 52.697	β = 90
c = 98.363	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Chen, Y., Li, C.-L., Hsiao, Y.-Y., Duh, Y., Yuan, H.S.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (Taiwan)	Taiwan	--

Revision History  

• 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: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.3: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description