1QZQ

human Tyrosyl DNA phosphodiesterase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Analysis of Human Tyrosyl-DNA Phosphodiesterase I Catalytic Residues.

Raymond, A.C.Rideout, M.C.Staker, B.Hjerrild, K.Burgin Jr., A.B.

(2004) J.Mol.Biol. 338: 895-906

  • DOI: 10.1016/j.jmb.2004.03.013

  • PubMed Abstract: 
  • Tyrosyl-DNA phosphodiesterase I (Tdp1) is involved in the repair of DNA lesions created by topoisomerase I in vivo. Tdp1 is a member of the phospholipase D (PLD) superfamily of enzymes and hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate D ...

    Tyrosyl-DNA phosphodiesterase I (Tdp1) is involved in the repair of DNA lesions created by topoisomerase I in vivo. Tdp1 is a member of the phospholipase D (PLD) superfamily of enzymes and hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate DNA and free tyrosine in vitro. Here, we use synthetic 3'-(4-nitro)phenyl, 3'-(4-methyl)phenyl, and 3'-tyrosine phosphate oligonucleotides to study human Tdp1. Kinetic analysis of human Tdp1 (hTdp1) shows that the enzyme has nanomolar affinity for all three substrates and the overall in vitro reaction is diffusion-limited. Analysis of active-site mutants using these modified substrates demonstrates that hTdp1 uses an acid/base catalytic mechanism. The results show that histidine 493 serves as the general acid during the initial transesterification, in agreement with hypotheses based on previous crystal structure models. The results also argue that lysine 495 and asparagine 516 participate in the general acid reaction, and the analysis of crystal structures suggests that these residues may function in a proton relay. Together with previous crystal structure data, the new functional data provide a mechanistic understanding of the conserved histidine, lysine and asparagine residues found among all PLD family members.


    Organizational Affiliation

    Biology Department, San Diego State University, CA 98182-4614, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tyrosyl-DNA phosphodiesterase 1
A, B
483Homo sapiensMutation(s): 0 
Gene Names: TDP1
EC: 3.1.4.-
Find proteins for Q9NUW8 (Homo sapiens)
Go to Gene View: TDP1
Go to UniProtKB:  Q9NUW8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.024α = 90.00
b = 105.131β = 90.00
c = 194.153γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MAR345data collection
SCALEPACKdata scaling
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation