5T2W: Thymine DNA glycosylase

Structure of thymine DNA glycosylase bound to substrate analog 2'-F-5-formyl-dC. Determined by X-ray diffraction at 2.2 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 2,977
Mol. weight: 43.12 kDa
Released: 9 Nov 2016

Explore 5T2W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T2W contains 11 α-helices and 8 β-strands across 1 chain. 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
α-helix	116-119	4
β-strand	127	1	1
β-strand	134-138	5	1
α-helix	143-148	6
β-strand	157	1	2
α-helix	159-165	7
α-helix	175-180	6
α-helix	181-185	5
β-strand	187-191	5	1
α-helix	200-202	3
α-helix	205-222	18
β-strand	226-230	5	1
α-helix	232-243	12
β-strand	253-254	2	1
α-helix	258-259	2
β-strand	265-269	5	1
β-strand	273	1	2
α-helix	282-284	3
α-helix	286-301	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G/T mismatch-specific thymine DNA glycosylase	A	protein	227	Homo sapiens	Q13569 (AlphaFold model)
DNA (28-mer)	C	DNA	28	synthetic construct
DNA (27-mer)	D	DNA	28	synthetic construct

Sequence of entity 1 (A), FASTA

>5T2W_1 G/T mismatch-specific thymine DNA glycosylase (chains A)
SKKSGKSAKSKEKQEKITDTFKVKRKVDRFNGVSEAELLTKTLPDILTFNLDIVIIGINP
GLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSK
DLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPD
TETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV

Sequence of entity 2 (C), FASTA

>5T2W_2 DNA (28-MER) (chains C)
CAGCTCTGTACGTGAGCGATGGACAGCT

Sequence of entity 3 (D), FASTA

>5T2W_3 DNA (27-MER) (chains D)
AGCTGTCCATCGCTCAXGTACAGAGCTG

Primary citation

Structural Basis for Excision of 5-Formylcytosine by Thymine DNA Glycosylase. Pidugu, L.S., Flowers, J.W., Coey, C.T. et al. Biochemistry (2016) 55:6205-6208. DOI 10.1021/acs.biochem.6b00982 · 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

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