4L5N: Uracil-DNA glycosylase

Crystallographic Structure of HHV-1 Uracil-DNA Glycosylase complexed with the Bacillus phage PZA inhibitor protein p56. Determined by X-ray diffraction at 2.16 Å resolution. Released 7 Aug 2013.

Method: X-ray diffraction
Resolution: 2.16 Å
Organisms: Herpes simplex virus type 1, Bacillus phage PZA
Chains: 6
Atoms: 5,681
Mol. weight: 80.67 kDa
Released: 7 Aug 2013

Explore 4L5N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4L5N contains 33 α-helices and 26 β-strands across 6 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: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	19-25	7
α-helix	30-32	3
α-helix	33-36	4
α-helix	37-41	5
α-helix	44-58	15
β-strand	61-62	2	1
α-helix	65-67	3
α-helix	70-72	3
α-helix	77-79	3
β-strand	82-86	5	2
α-helix	108-110	3
α-helix	111-123	13
α-helix	136-140	5
β-strand	143-147	5	2
β-strand	152-153	2	1
β-strand	156	1	1
α-helix	165-179	15
β-strand	184-188	5	2
α-helix	190-195	6
β-strand	204-208	5	2
α-helix	219-221	3
α-helix	224-234	11
α-helix	238-240	3

Chain B: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	19-26	8
α-helix	30-32	3
α-helix	33-41	9
α-helix	43-56	14
β-strand	61-62	2	3
α-helix	70-72	3
β-strand	82-86	5	4
α-helix	108-110	3
α-helix	111-123	13
α-helix	136-140	5
β-strand	143-147	5	4
β-strand	152-153	2	3
β-strand	156	1	3
α-helix	165-179	15
β-strand	184-188	5	4
α-helix	190-195	6
β-strand	204-208	5	4
α-helix	219-221	3
α-helix	224-234	11
α-helix	237-240	4

Chain C: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	5
β-strand	23-31	9	5
α-helix	33-42	10
β-strand	46-54	9	5

Chains D, E and F: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	5
β-strand	23-31	9	5
α-helix	33-41	9
β-strand	46-54	9	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uracil-DNA glycosylase	A, B	protein	241	Herpes simplex virus type 1	P10186
Early protein GP1B	C, D, E, F	protein	55	Bacillus phage PZA	P06948

Sequence of entity 1 (A, B), FASTA

>4L5N_1 Uracil-DNA glycosylase (chains A, B)
STGGVSPAATSAPLDWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEEVLP
PREDVFSWTRYCTPDEVRVVIIGQDPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAVKNC
YPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARRPGL
VFMLWGTHAQNAIRPDPRVHCVLKFSHPSPLSKVPFGTCQHFLVANRYLETRSISPIDWS
V

Sequence of entity 2 (C, D, E, F), FASTA

>4L5N_2 Early protein GP1B (chains C, D, E, F)
VQNDFLDSYDVTMLLQDDNGKQYYEYHKGLSLSDFEVLYGNTVDEIIKLRVDKIS

Primary citation

Architecturally diverse proteins converge on an analogous mechanism to inactivate Uracil-DNA glycosylase. Cole, A.R., Ofer, S., Ryzhenkova, K. et al. Nucleic Acids Res (2013) 41:8760-8775. DOI 10.1093/nar/gkt633 · PubMed

Other PDB entries of the same protein (UniProt P10186), best resolution first:

1UDG 1.75 Å, The structural basis of specific base excision repair by uracil-DNA glycosylase
1UDH 1.75 Å, The structural basis of specific base excision repair by uracil-DNA glycosylase
1LAU 1.8 Å, Uracil-DNA glycosylase
2C53 1.8 Å, A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1
5AYS 2.09 Å, Crystal structure of SAUGI/HSV UDG complex
2C56 2.1 Å, A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1
1UDI 2.7 Å, Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil…

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