1EMH: Human uracil-DNA glycosylase

Crystal structure of human uracil-DNA glycosylase bound to uncleaved substrate-containing DNA. Determined by X-ray diffraction at 1.8 Å resolution. Released 16 May 2000.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,362
Mol. weight: 31.31 kDa
Released: 16 May 2000

Explore 1EMH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1EMH contains 15 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: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	87-93	7
α-helix	94-96	3
α-helix	100-115	16
β-strand	118-119	2	1
α-helix	122-124	3
α-helix	127-129	3
α-helix	134-136	3
β-strand	139-143	5	2
α-helix	165-167	3
α-helix	168-180	13
α-helix	193-196	4
β-strand	200-204	5	2
β-strand	209-210	2	1
α-helix	222-236	15
β-strand	241-245	5	2
α-helix	247-250	4
α-helix	251-255	5
β-strand	262-266	5	2
α-helix	274-276	3
α-helix	283-293	11
α-helix	296-299	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-D(TPGPTP(P2U)PAPTPCPTP*T)-3')	B	DNA	9
DNA (5'-d(apapapgpaptpapapcpa)-3')	C	DNA	10
Uracil-DNA glycosylase	A	protein	223	Homo sapiens	P13051 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>1EMH_1 DNA (5'-D(*TP*GP*TP*(P2U)P*AP*TP*CP*TP*T)-3') (chains B)
TGTUATCTT

Sequence of entity 2 (C), FASTA

>1EMH_2 DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3') (chains C)
AAAGATAACA

Sequence of entity 3 (A), FASTA

>1EMH_3 URACIL-DNA GLYCOSYLASE (chains A)
MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVI
LGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVL
LLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRH
HVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL

Primary citation

Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. Parikh, S.S., Walcher, G., Jones, G.D. et al. Proc Natl Acad Sci U S A (2000) 97:5083-5088. DOI 10.1073/pnas.97.10.5083 · PubMed

Other PDB entries of the same protein (UniProt P13051 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FCI 1.27 Å, Complex of UNG2 and a fragment-based designed inhibitor
2HXM 1.3 Å, Complex of UNG2 and a small Molecule synthetic Inhibitor
3TKB 1.5 Å, crystal structure of human uracil-DNA glycosylase D183G/K302R mutant
1AKZ 1.57 Å, Human uracil-DNA glycosylase
3FCK 1.64 Å, Complex of UNG2 and a fragment-based design inhibitor
3FCL 1.7 Å, Complex of UNG2 and a fragment-based designed inhibitor
9LNQ 1.74 Å, The hUNG bound to DNA product embedding 4primer-OCH3-dU
9LNP 1.76 Å, the hUNG bound to DNA product embedding uridine ribonucleotide
6VBA 1.8 Å, Structure of human Uracil DNA Glycosylase (UDG) bound to Aurintricarboxylic acid (ATA)
3FCF 1.84 Å, Complex of UNG2 and a fragment-based designed inhibitor
1Q3F 1.9 Å, Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA
1SSP 1.9 Å, Wild-type uracil-DNA glycosylase bound to uracil-containing DNA

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