4Z3A: G/T mismatch-specific thymine DNA glycosylase

Acetate-free structure of the enzyme-product complex resulting from TDG action on a GU mismatch. Determined by X-ray diffraction at 1.72 Å resolution. Released 16 Sept 2015.

Method: X-ray diffraction
Resolution: 1.72 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 2,944
Mol. weight: 40.19 kDa
Released: 16 Sept 2015

Explore 4Z3A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Z3A contains 11 α-helices and 6 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	108-111	4
α-helix	116-120	5
β-strand	127	1	1
β-strand	134-138	5	1
α-helix	143-148	6
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	232-242	11
β-strand	253-258	6	1
α-helix	259	1
β-strand	265-269	5	1
α-helix	282-299	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G/T mismatch-specific thymine DNA glycosylase	A	protein	204	Homo sapiens	Q13569 (AlphaFold model)
DNA (28-mer)	C	DNA	28	synthetic construct
DNA (28-mer)	D	DNA	28	synthetic construct

Sequence of entity 1 (A), FASTA

>4Z3A_1 G/T mismatch-specific thymine DNA glycosylase (chains A)
GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLF
MSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQP
RIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQD
KVHYYIKLKDLRDQLKGIERNMDV

Sequence of entity 2 (C), FASTA

>4Z3A_2 DNA (28-MER) (chains C)
CAGCTCTGTACGTGAGCGATGGACAGCT

Sequence of entity 3 (D), FASTA

>4Z3A_3 DNA (28-MER) (chains D)
AGCTGTCCATCGCTCAXGTACAGAGCTG

Primary citation

Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA. Malik, S.S., Coey, C.T., Varney, K.M. et al. Nucleic Acids Res (2015) 43:9541-9552. DOI 10.1093/nar/gkv890 · 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
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
5T2W 2.2 Å, Structure of thymine DNA glycosylase bound to substrate analog 2'-F-5-formyl-dC

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