5CYS: G/T mismatch-specific thymine DNA glycosylase

Structure of the enzyme-product complex resulting from TDG action on a GcaC mismatch. Determined by X-ray diffraction at 2.45 Å resolution. Released 16 Sept 2015.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 2,948
Mol. weight: 40.25 kDa
Released: 16 Sept 2015

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

Secondary structure: helices and β-sheets

5CYS contains 9 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: 9 helices, 6 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
α-helix	159-165	7
α-helix	175-180	6
α-helix	181-185	5
β-strand	187-191	5	1
α-helix	205-222	18
β-strand	226-230	5	1
α-helix	232-243	12
β-strand	253-258	6	1
α-helix	259	1
β-strand	265-269	5	1
α-helix	286-302	17

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

>5CYS_1 G/T mismatch-specific thymine DNA glycosylase (chains A)
GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLF
MSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQP
RIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQD
KVHYYIKLKDLRDQLKGIERNMDV

Sequence of entity 2 (C), FASTA

>5CYS_2 DNA (28-MER) (chains C)
CAGCTCTGTACGTGAGCGATGGACAGCT

Sequence of entity 3 (D), FASTA

>5CYS_3 DNA (28-MER) (chains D)
AGCTGTCCATCGCTCAXGTACAGAGCTG

Primary citation

Characterizing the enzyme-product complexes of thymine DNA glycosylase using crystallography and NMR. Malik, S.S., Varney, K.M., Pozharski, E. et al. Nucleic Acids Res (2015).

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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