3UO7: Human Thymine DNA Glycosylase

Crystal structure of Human Thymine DNA Glycosylase Bound to Substrate 5-carboxylcytosine. Determined by X-ray diffraction at 3.0 Å resolution. Released 15 Feb 2012.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,761
Mol. weight: 59.61 kDa
Released: 15 Feb 2012

Explore 3UO7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3UO7 contains 20 α-helices and 14 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	127	1	1
β-strand	134-138	5	1
α-helix	143-148	6
β-strand	157	1	2
α-helix	159-166	8
α-helix	175-180	6
β-strand	187-191	5	1
α-helix	205-222	18
β-strand	226-230	5	1
α-helix	232-238	7
α-helix	239-243	5
α-helix	250-251	2
β-strand	253-258	6	1
α-helix	259	1
α-helix	264	1
β-strand	265-269	5	1
β-strand	273	1	2
α-helix	282-284	3
α-helix	286-301	16

Chain B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	127	1	3
β-strand	134-138	5	3
α-helix	143-148	6
α-helix	159-166	8
α-helix	175-180	6
α-helix	181-185	5
β-strand	187-191	5	3
α-helix	205-222	18
β-strand	226-231	6	3
α-helix	233-238	6
α-helix	239-243	5
β-strand	253-258	6	3
β-strand	265-269	5	3
α-helix	283-285	3
α-helix	286-301	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(cpapgpcptpcptpgptpapcpaptpgpapgpcpapgptpgpgp*a)-3'	C	DNA	23
5'-D(CPCPAPCPTPGPCPTPCPAP(1CC)PGPTPAPCPAPGPAPGPCPTPGP*T)-3'	D	DNA	23
G/T mismatch-specific thymine DNA glycosylase	A, B	protein	201	Homo sapiens	Q13569 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>3UO7_1 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*AP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3' (chains C)
CAGCTCTGTACATGAGCAGTGGA

Sequence of entity 2 (D), FASTA

>3UO7_2 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1CC)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3' (chains D)
CCACTGCTCAXGTACAGAGCTGT

Sequence of entity 3 (A, B), FASTA

>3UO7_3 G/T mismatch-specific thymine DNA glycosylase (chains A, B)
SNAFNGVSEAELLTKTLPDILTFNLDIVIIGIAPGLMAAYKGHHYPGPGNHFWKCLFMSG
LSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIA
VFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVH
YYIKLKDLRDQLKGIERNMDV

Primary citation

Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Zhang, L., Lu, X., Lu, J. et al. Nat Chem Biol (2012) 8:328-330. DOI 10.1038/nchembio.914 · PubMed

Other PDB entries of the same protein (UniProt Q13569 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4Z47 1.45 Å, Structure of the enzyme-product complex resulting from TDG action on a GU mismatch in…
5HF7 1.54 Å, TDG enzyme-substrate complex
6U17 1.55 Å, Human thymine DNA glycosylase bound to DNA with 2'-F-5-carboxyl-dC substrate analog
6U16 1.6 Å, Human thymine DNA glycosylase N140A mutant bound to DNA with 5-carboxyl-dC substrate
5FF8 1.7 Å, TDG enzyme-product complex
5JXY 1.71 Å, Enzyme-substrate complex of TDG catalytic domain bound to a G/U analog
4XEG 1.72 Å, Structure of the enzyme-product complex resulting from TDG action on a G/hmU mismatch
4Z3A 1.72 Å, Acetate-free structure of the enzyme-product complex resulting from TDG action on a GU…
4Z7Z 1.83 Å, Structure of the enzyme-product complex resulting from TDG action on a GT mismatch in…
4Z7B 2.02 Å, Structure of the enzyme-product complex resulting from TDG action on a GfC mismatch
1WYW 2.1 Å, Crystal Structure of SUMO1-conjugated thymine DNA glycosylase
2D07 2.1 Å, Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase

Browse structure collections

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