5AYS: SAUGI/HSV UDG complex

Crystal structure of SAUGI/HSV UDG complex. Determined by X-ray diffraction at 2.09 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 2.09 Å
Organisms: Human herpesvirus 1 (strain 17), Staphylococcus aureus
Chains: 4
Atoms: 6,232
Mol. weight: 84.58 kDa
Released: 8 Jun 2016

Explore 5AYS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AYS contains 44 α-helices and 26 β-strands across 4 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	19-26	8
α-helix	30-32	3
α-helix	33-36	4
α-helix	37-41	5
α-helix	43-58	16
β-strand	61-62	2	1
α-helix	65-67	3
α-helix	71-74	4
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: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	19-26	8
α-helix	30-32	3
α-helix	33-36	4
α-helix	37-41	5
α-helix	43-58	16
β-strand	61-62	2	4
α-helix	65-68	4
α-helix	71-74	4
α-helix	77-79	3
β-strand	82-86	5	5
α-helix	108-109	2
α-helix	111-123	13
α-helix	136-140	5
β-strand	143-147	5	5
β-strand	152-153	2	4
β-strand	156	1	4
α-helix	165-179	15
β-strand	184-188	5	5
α-helix	190-195	6
β-strand	204-208	5	5
α-helix	219-221	3
α-helix	224-234	11
α-helix	238-240	3

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	22-23	2
β-strand	24-31	8	3
α-helix	32-34	3
α-helix	38-40	3
β-strand	50-57	8	3
α-helix	59-64	6
β-strand	67-73	7	3
β-strand	76-83	8	3
β-strand	89-95	7	3
β-strand	100-103	4	3
α-helix	105-108	4

Chain D: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	22-23	2
β-strand	24-31	8	6
α-helix	32-34	3
α-helix	38-40	3
β-strand	50-57	8	6
α-helix	59-64	6
β-strand	67-73	7	6
β-strand	76-83	8	6
β-strand	89-95	7	6
β-strand	100-103	4	6
α-helix	105-108	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uracil-DNA glycosylase	A, B	protein	256	Human herpesvirus 1 (strain 17)	P10186
Uncharacterized protein	C, D	protein	112	Staphylococcus aureus	Q936H5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5AYS_1 Uracil-DNA glycosylase (chains A, B)
MDLTNGGVSPAATSAPLDWTTFRRVFLIDDAWRPLMEPELANPLTAHLLAEYNRRCQTEE
VLPPREDVFSWTRYCTPDEVRVVIIGQDPYHHPGQAHGLAFSVRANVPPPPSLRNVLAAV
KNCYPEARMSGHGCLEKWARDGVLLLNTTLTVKRGAAASHSRIGWDRFVGGVIRRLAARR
PGLVFMLWGTHAQNAIRPDPRVHCVLKFSHPSPLSKVPFGTCQHFLVANRYLETRSISPI
DWSVLEELLEHHHHHH

Sequence of entity 2 (C, D), FASTA

>5AYS_2 Uncharacterized protein (chains C, D)
MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDT
LHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLTGGQ

Primary citation

Using structural-based protein engineering to modulate the differential inhibition effects of SAUGI on human and HSV uracil DNA glycosylase. Wang, H.C., Ho, C.H., Chou, C.C. et al. Nucleic Acids Res (2016) 44:4440-4449. DOI 10.1093/nar/gkw185 · 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
2C56 2.1 Å, A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1
4L5N 2.16 Å, Crystallographic Structure of HHV-1 Uracil-DNA Glycosylase complexed with the Bacillus…
1UDI 2.7 Å, Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil…

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