ISDA: 3UOB

Deposition Date 2011-11-16

Release Date 2012-02-15

Last Version Date 2023-09-13

Entry Detail

PDB ID:

3UOB

Keywords:

HYDROLASE/DNA

Title:

Crystal structure of Human Thymine DNA Glycosylase Bound to Substrate Analog 2'-deoxy-2'-beta-fluoro-cytidine

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.01 Å

R-Value Free:

0.27

R-Value Work:

0.21

R-Value Observed:

0.22

Space Group:

P 65

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:G/T mismatch-specific thymine DNA glycosylase
Gene (Uniprot):TDG
Chain IDs:C (auth: A), D (auth: B)
Chain Length:201
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q13569 Pfam ID:PF03167 EC:3.2.2.29

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
1FC	B	DC	?

Ligand Molecules

Primary Citation

Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA.

Zhang, L, Lu, X, Lu, J, Liang, H, Dai, Q, Xu, G.L, Luo, C, Jiang, H, He, C.Show

Nat.Chem.Biol. 8 328 330 (2012)

PMID: 22327402 DOI: 10.1038/nchembio.914

Abstact

Human thymine DNA glycosylase (hTDG) efficiently excises 5-carboxylcytosine (5caC), a key oxidation product of 5-methylcytosine in genomic DNA, in a recently discovered cytosine demethylation pathway. We present here the crystal structures of the hTDG catalytic domain in complex with duplex DNA containing either 5caC or a fluorinated analog. These structures, together with biochemical and computational analyses, reveal that 5caC is specifically recognized in the active site of hTDG, supporting the role of TDG in mammalian 5-methylcytosine demethylation.

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Primary Citation of related structures