3UFJ: Human Thymine DNA Glycosylase

Human Thymine DNA Glycosylase Bound to Substrate Analog 2'-fluoro-2'-deoxyuridine. Determined by X-ray diffraction at 2.97 Å resolution. Released 25 Apr 2012.

Method: X-ray diffraction
Resolution: 2.97 Å
Organism: Homo sapiens
Chains: 6
Atoms: 4,509
Mol. weight: 74.43 kDa
Released: 25 Apr 2012

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

Secondary structure: helices and β-sheets

3UFJ contains 19 α-helices and 12 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: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	124-126	3
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
α-helix	181-185	5
β-strand	187-191	5	1
α-helix	205-222	18
β-strand	226-230	5	1
α-helix	232-238	7
α-helix	239-243	5
β-strand	253-255	3	1
α-helix	258-259	2
β-strand	265-269	5	1
β-strand	273	1	2
α-helix	287-301	15

Chain B: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	134-138	5	3
α-helix	143-148	6
α-helix	159-163	5
α-helix	164-168	5
α-helix	175-180	6
α-helix	181-185	5
β-strand	187-191	5	3
α-helix	206-222	17
β-strand	226-230	5	3
α-helix	232-238	7
α-helix	239-243	5
β-strand	253-258	6	3
β-strand	265-269	5	3
α-helix	287-301	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G/T mismatch-specific thymine DNA glycosylase	A, B	protein	204	Homo sapiens	Q13569 (AlphaFold model)
5'-d(cpapgpcptpcptpgptpapcpgptpgpapgpcpapgptpgpgp*a)-3'	C, E	DNA	23
5'-D(CPCPAPCPTPGPCPTPCPAP(UF2)PGPTPAPCPAPGPAPGPCPTPGP*T)-3'	D, F	DNA	23

Sequence of entity 1 (A, B), FASTA

>3UFJ_1 G/T mismatch-specific thymine DNA glycosylase (chains A, B)
GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLF
MSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQP
RIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQD
KVHYYIKLKDLRDQLKGIERNMDV

Sequence of entity 2 (C, E), FASTA

>3UFJ_2 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP*GP*TP*GP*GP*A)-3' (chains C, E)
CAGCTCTGTACGTGAGCAGTGGA

Sequence of entity 3 (D, F), FASTA

>3UFJ_3 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(UF2)P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3' (chains D, F)
CCACTGCTCAXGTACAGAGCTGT

Primary citation

Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA. Maiti, A., Noon, M.S., Mackerell, A.D. et al. Proc Natl Acad Sci U S A (2012) 109:8091-8096. DOI 10.1073/pnas.1201010109 · 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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