2RBA: Human Thymine DNA Glycosylase

Structure of Human Thymine DNA Glycosylase Bound to Abasic and Undamaged DNA. Determined by X-ray diffraction at 2.79 Å resolution. Released 17 Jun 2008.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,845
Mol. weight: 60.16 kDa
Released: 17 Jun 2008

Explore 2RBA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2RBA contains 21 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: 10 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	159-165	7
α-helix	178-180	3
α-helix	181-185	5
β-strand	187-191	5	1
α-helix	205-222	18
β-strand	226-230	5	1
α-helix	232-242	11
α-helix	250-251	2
β-strand	253-254	2	1
α-helix	257-259	3
β-strand	265-269	5	1
β-strand	273	1	2
α-helix	282-284	3
α-helix	286-299	14

Chain B: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	124-126	3
β-strand	127	1	3
β-strand	134-138	5	3
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	3
α-helix	200-202	3
α-helix	205-222	18
β-strand	226-230	5	3
α-helix	231-242	12
β-strand	253-258	6	3
α-helix	259	1
α-helix	264	1
β-strand	265-269	5	3
α-helix	286-301	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(dcpdapdgpdcpdtpdcpdtpdgpdtpdapdcpdgpdtpdgpdapdgpdcpdapdgpdtpdgpdgp*…	C	DNA	23
DNA (5'-D(DCPDCPDAPDCPDTPDGPDCPDTPDCPDAP(3DR)PDGPDTPDAPDCPDAPDGPDAPDGPDCPDTPD…	D	DNA	23
G/T mismatch-specific thymine DNA glycosylase	A, B	protein	204	Homo sapiens	Q13569 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>2RBA_1 DNA (5'-D(*DCP*DAP*DGP*DCP*DTP*DCP*DTP*DGP*DTP*DAP*DCP*DGP*DTP*DGP*DAP*DGP*DCP*DAP*DGP*DTP*DGP*DGP*DA)-3') (chains C)
CAGCTCTGTACGTGAGCAGTGGA

Sequence of entity 2 (D), FASTA

>2RBA_2 DNA (5'-D(*DCP*DCP*DAP*DCP*DTP*DGP*DCP*DTP*DCP*DAP*(3DR)P*DGP*DTP*DAP*DCP*DAP*DGP*DAP*DGP*DCP*DTP*DGP*DT)-3') (chains D)
CCACTGCTCANGTACAGAGCTGT

Sequence of entity 3 (A, B), FASTA

>2RBA_3 G/T mismatch-specific thymine DNA glycosylase (chains A, B)
GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLF
MSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQP
RIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQD
KVHYYIKLKDLRDQLKGIERNMDV

Primary citation

Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition. Maiti, A., Morgan, M.T., Pozharski, E. et al. Proc Natl Acad Sci U S A (2008) 105:8890-8895. DOI 10.1073/pnas.0711061105 · 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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