6LYV | pdb_00006lyv

The crystal structure of SAUGI/KSHVUDG complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8076598	3001106	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8076598	3001106	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8076598	3001106	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8076598	3001106	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8076598	3001106	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8076598	3001106	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8076598	3001106	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Uracil-DNA glycosylase-like	8076598	3001106	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8054183	3000500	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8054183	3000500	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8054183	3000500	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8054183	3000500	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8054183	3000500	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8054183	3000500	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8054183	3000500	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Uracil-DNA glycosylase inhibitor protein	8054183	3000500	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	UDG	e6lyvA1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
C	UDG	e6lyvC1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
E	UDG	e6lyvE1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
G	UDG	e6lyvG1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
I	UDG	e6lyvI1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
K	UDG	e6lyvK1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
M	UDG	e6lyvM1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
O	UDG	e6lyvO1	A: a/b three-layered sandwiches	X: Uracil-DNA glycosylase-like (From Topology)	H: Uracil-DNA glycosylase-like (From Topology)	T: Uracil-DNA glycosylase-like	F: UDG	ECOD (1.6)
B	SAUGI	e6lyvB1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: SAUGI	ECOD (1.6)
D	SAUGI	e6lyvD1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: SAUGI	ECOD (1.6)
F	SAUGI	e6lyvF1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: SAUGI	ECOD (1.6)
H	SAUGI	e6lyvH1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: SAUGI	ECOD (1.6)
J	SAUGI	e6lyvJ1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: SAUGI	ECOD (1.6)
L	SAUGI	e6lyvL1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: SAUGI	ECOD (1.6)
N	SAUGI	e6lyvN1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: SAUGI	ECOD (1.6)
P	SAUGI	e6lyvP1	A: a+b two layers	X: Cystatin-like	H: Uracil-DNA glycosylase inhibitor protein (From Topology)	T: Uracil-DNA glycosylase inhibitor protein	F: SAUGI	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (utative)
C	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (utative)
E	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (utative)
G	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (utative)
I	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (utative)
K	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (utative)
M	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (utative)
O	3.40.470.10	Alpha Beta	3-Layer(aba) Sandwich	Uracil-DNA Glycosylase, subunit E	Uracil-DNA glycosylase-like domain	CATH (utative)
B	3.10.450.250	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)
D	3.10.450.250	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)
F	3.10.450.250	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)
H	3.10.450.250	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)
J	3.10.450.250	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)
L	3.10.450.250	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)
N	3.10.450.250	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)
P	3.10.450.250	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K, M, O	PF03167	Uracil DNA glycosylase superfamily (UDG)	Uracil DNA glycosylase superfamily		Domain
B, D, F, H, J B, D, F, H, J, L, N, P	PF06106	S. aureus uracil DNA glycosylase inhibitor (SAUGI)	S. aureus uracil DNA glycosylase inhibitor	Uracil-DNA glycosylase inhibitors, are DNA mimic proteins that prevent the DNA binding sites of UDGs (Uracil DNA glycosylase) from interacting with their DNA substrate. SSP0047 Swiss:Q4A134 (or SAUGI; for Staphylococcus aureus uracil-DNA glycosylase ...	Uracil-DNA glycosylase inhibitors, are DNA mimic proteins that prevent the DNA binding sites of UDGs (Uracil DNA glycosylase) from interacting with their DNA substrate. SSP0047 Swiss:Q4A134 (or SAUGI; for Staphylococcus aureus uracil-DNA glycosylase inhibitor) acts as a uracil-DNA glycosylase inhibitor that breaks the uracil-removing activity of S. aureus uracil-DNA glycosylase (SAUDG) Pfam:PF03167 [1]. The SAUGI/SAUDG complex has been determined, and shows that SAUGI binds to the SAUDG DNA binding region via several strong interactions, by using a hydrophobic pocket to hold SAUDG's protruding residue (i.e. SAUDG Leu184, E. coli UDG Leu191 and B. subtilis UDG Phe191). By binding to SAUDG in this way, SAUGI thus prevents SAUDG from binding to its DNA substrate and performing DNA repair activity [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K, M, O	Uracil-DNA glycosylase	uracil DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds deaminated base DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity	cellular response to stimulus response to stimulus base-excision repair, AP site formation via deaminated base removal primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus base-excision repair, AP site formation via deaminated base removal primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process base-excision repair, AP site formation DNA repair	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus host intracellular organelle
B, D, F, H, J B, D, F, H, J, L, N, P	SAUGI	cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR002043	Uracil-DNA glycosylase family 1	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR018085	Uracil-DNA glycosylase, active site	Active Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036895	Uracil-DNA glycosylase-like domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR005122	Uracil-DNA glycosylase-like	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR043068	Uracil DNA glycosylase inhibitor superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR009295	S. aureus uracil DNA glycosylase inhibitor	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.