4JGC

Human TDG N140A mutant IN A COMPLEX WITH 5-carboxylcytosine (5caC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.582 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Activity and crystal structure of human thymine DNA glycosylase mutant N140A with 5-carboxylcytosine DNA at low pH.

Hashimoto, H.Zhang, X.Cheng, X.

(2013) Dna Repair 12: 535-540

  • DOI: 10.1016/j.dnarep.2013.04.003

  • PubMed Abstract: 
  • The mammalian thymine DNA glycosylase (TDG) excises 5-carboxylcytosine (5caC) when paired with a guanine in a CpG sequence, in addition to mismatched bases. Here we present a complex structure of the human TDG catalytic mutant, asparagine 140 to alan ...

    The mammalian thymine DNA glycosylase (TDG) excises 5-carboxylcytosine (5caC) when paired with a guanine in a CpG sequence, in addition to mismatched bases. Here we present a complex structure of the human TDG catalytic mutant, asparagine 140 to alanine (N140A), with a 28-base pair DNA containing a G:5caC pair at pH 4.6. TDG interacts with the carboxylate moiety of target nucleotide 5caC using the side chain of asparagine 230 (N230), instead of asparagine 157 (N157) as previously reported. Mutation of either N157 or N230 residues to aspartate has minimal effect on G:5caC activity while significantly reducing activity on G:U substrate. Combination of both the asparagine-to-aspartate mutations (N157D/N230D) resulted in complete loss of activity on G:5caC while retaining measurable activity on G:U, implying that 5caC can adopt alternative conformations (either N157-interacting or N230-interacting) in the TDG active site to interact with either of the two asparagine side chain for 5caC excision.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA. hhashi3@emory.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
G/T mismatch-specific thymine DNA glycosylase
A
204Homo sapiensGene Names: TDG
EC: 3.2.2.29
Find proteins for Q13569 (Homo sapiens)
Go to Gene View: TDG
Go to UniProtKB:  Q13569
Entity ID: 2
MoleculeChainsLengthOrganism
oligonucleotideC28N/A
Entity ID: 3
MoleculeChainsLengthOrganism
oligonucleotide containing 5-carboxylcytosineD28N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1RT
Query on 1RT

Download SDF File 
Download CCD File 
D
4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid
C5 H5 N3 O3
BLQMCTXZEMGOJM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ORP
Query on ORP
D
SACCHARIDEC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.582 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.486α = 90.00
b = 53.555β = 95.10
c = 81.902γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references