1LQM: Uracil-DNA glycosylase

Escherichia coli uracil-DNA glycosylase complex with uracil-DNA glycosylase inhibitor protein. Determined by X-ray diffraction at 3.2 Å resolution. Released 10 Nov 2002.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Escherichia coli, Bacillus phage PBS2
Chains: 8
Atoms: 9,744
Mol. weight: 140.83 kDa
Released: 10 Nov 2002

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

Secondary structure: helices and β-sheets

1LQM contains 66 α-helices and 53 β-strands across 8 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: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	14-16	3
α-helix	18-33	16
β-strand	37-38	2	1
α-helix	41-44	4
α-helix	46-50	5
α-helix	53-55	3
β-strand	58-62	5	2
β-strand	72	1	3
β-strand	79	1	3
α-helix	84-86	3
α-helix	87-99	13
α-helix	112-116	5
β-strand	119-123	5	2
β-strand	128-129	2	1
β-strand	132	1	1
α-helix	141-155	15
β-strand	160-164	5	2
α-helix	166-171	6
α-helix	172-174	3
β-strand	181-185	5	2
α-helix	190-192	3
α-helix	193-197	5
α-helix	202-211	10

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	20-24	5	4
α-helix	26-32	7
β-strand	41-48	8	4
β-strand	53-60	8	4
β-strand	67-74	8	4
β-strand	79-83	5	4

Chain C: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	14-16	3
α-helix	18-32	15
β-strand	37-38	2	5
α-helix	41-43	3
α-helix	46-50	5
β-strand	58-62	5	6
α-helix	84-86	3
α-helix	89-99	11
α-helix	112-116	5
β-strand	119-123	5	6
β-strand	128-129	2	5
β-strand	132	1	5
α-helix	141-155	15
β-strand	160-164	5	6
α-helix	166-171	6
β-strand	181-185	5	6
α-helix	190-192	3
α-helix	193-197	5
α-helix	202-211	10

Chain D: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	18	1	7
β-strand	22-24	3	7
α-helix	26-33	8
β-strand	41-48	8	7
β-strand	53-60	8	7
β-strand	67-74	8	7
β-strand	79-83	5	7

Chain E: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	14-16	3
α-helix	18-32	15
β-strand	37-38	2	8
α-helix	40	1
α-helix	46-50	5
α-helix	53-55	3
β-strand	58-62	5	9
β-strand	72	1	10
β-strand	79	1	10
α-helix	84-86	3
α-helix	87-99	13
α-helix	112-117	6
β-strand	119-123	5	9
β-strand	128-129	2	8
β-strand	132	1	8
α-helix	141-155	15
β-strand	160-164	5	9
α-helix	166-172	7
β-strand	181-185	5	9
α-helix	190-192	3
α-helix	193-197	5
α-helix	202-211	10
α-helix	215-218	4

Chains F and H: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	20-24	5	11
α-helix	26-33	8
β-strand	41-48	8	11
β-strand	53-60	8	11
β-strand	67-73	7	11
β-strand	79-83	5	11

Chain G: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	14-16	3
α-helix	18-32	15
β-strand	37-38	2	12
α-helix	41-43	3
α-helix	46-50	5
α-helix	53-55	3
β-strand	58-62	5	13
α-helix	84-86	3
α-helix	87-99	13
α-helix	112-115	4
β-strand	119-123	5	13
β-strand	128-129	2	12
β-strand	132	1	12
α-helix	141-155	15
β-strand	160-164	5	13
α-helix	166-172	7
β-strand	181-185	5	13
α-helix	193-195	3
α-helix	202-211	10
α-helix	215-218	4
α-helix	222-223	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uracil-DNA glycosylase	A, C, E, G	protein	229	Escherichia coli	P12295 (AlphaFold model)
Uracil-DNA glycosylase inhibitor	B, D, F, H	protein	84	Bacillus phage PBS2	P14739 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>1LQM_1 URACIL-DNA GLYCOSYLASE (chains A, C, E, G)
MANELTWHDVLAEEKQQPYFLNTLQTVASERQSGVTIYPPQKDVFNAFRFTELGDVKVVI
LGQDPYHGPGQAHGLAFSVRPGIAIPPSLLNMYKELENTIPGFTRPNHGYLESWARQGVL
LLNTVLTVRAGQAHSHASLGWETFTDKVISLINQHREGVVFLLWGSHAQKKGAIIDKQRH
HVLKAPHPSPLSAHRGFFGCNHFVLANQWLEQRGETPIDWMPVLPAESE

Sequence of entity 2 (B, D, F, H), FASTA

>1LQM_2 URACIL-DNA GLYCOSYLASE INHIBITOR (chains B, D, F, H)
MTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTS
DAPEYKPWALVIQDSNGENKIKML

Primary citation

Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG. Saikrishnan, K., Bidya Sagar, M., Ravishankar, R. et al. Acta Crystallogr D Biol Crystallogr (2002) 58:1269-1276. DOI 10.1107/S0907444902009599 · PubMed

Other PDB entries of the same protein (UniProt P12295 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3UF7 1.2 Å, Co-crystal structure of Escherichia coli uracil-DNA glycosylase and a C-terminal…
4EUG 1.4 Å, Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia…
3EUG 1.43 Å, Crystal structure of escherichia coli uracil DNA glycosylase and its complexes with…
2EUG 1.5 Å, Crystal structure of escherichia coli uracil DNA glycosylase and its complexes with…
1EUG 1.6 Å, Crystal structure of escherichia coli uracil DNA glycosylase and its complexes with…
5EUG 1.6 Å, Crystallographic and enzymatic studies of an active site variant H187Q of escherichia…
1FLZ 2.3 Å, Uracil DNA glycosylase with uaap
1UUG 2.4 Å, Escherichia coli uracil-DNA glycosylase:inhibitor complex with wild-type udg and…
2UUG 2.6 Å, Escherichia coli uracil-DNA glycosylase:inhibitor complex with H187D mutant udg and…
1LQG 2.9 Å, Escherichia coli uracil-DNA glycosylase complex with uracil-DNA glycosylase inhibitor…
1EUI 3.2 Å, Escherichia coli uracil-DNA glycosylase complex with uracil-DNA glycosylase inhibitor…
1LQJ 3.35 Å, Escherichia coli uracil-DNA glycosylase

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