1EUG

CRYSTAL STRUCTURE OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE AND ITS COMPLEXES WITH URACIL AND GLYCEROL: STRUCTURE AND GLYCOSYLASE MECHANISM REVISITED

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1euga_	Alpha and beta proteins (a/b)	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase-like	Uracil-DNA glycosylase	Uracil-DNA glycosylase	(Escherichia coli B ) [TaxId: 37762 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Uracil-DNA glycosylase	8031630	4003601	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Uracil-DNA glycosylase-like	8044008	3001106	SCOP2 (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	e1eugA1	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)

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 (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03167	Uracil DNA glycosylase superfamily (UDG)	Uracil DNA glycosylase superfamily	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PROTEIN (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 nucleobase-containing compound metabolic process base-excision repair organic substance metabolic process heterocycle metabolic process cellular response to stress response to stress nitrogen compound metabolic process DNA repair cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process cellular response to stimulus response to stimulus base-excision repair, AP site formation via deaminated base removal nucleobase-containing compound metabolic process base-excision repair organic substance metabolic process heterocycle metabolic process cellular response to stress response to stress nitrogen compound metabolic process DNA repair cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process organic cyclic compound metabolic process DNA damage response metabolic process cellular process macromolecule metabolic process base-excision repair, AP site formation cellular aromatic compound metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002043	Uracil-DNA glycosylase family 1	Family
A	IPR018085	Uracil-DNA glycosylase, active site	Active Site
A	IPR036895	Uracil-DNA glycosylase-like domain superfamily	Homologous Superfamily
A	IPR005122	Uracil-DNA glycosylase-like	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	uridine nucleosidase (family I) M-CSA #71	Uracil-DNA glycosylase (UDG) are monofunctional glycosylases and initiate the base excision repair (BER) pathway for uracil by hydrolysing the N-C'1 glycosylic bond between a target uracil and an abasic site. The human BER cycle is important for restoring the chemical integrity of DNA. The uracil-DNA glycosylase superfamily consists of 6 smaller families, based on sequence alignments. Both human and E.coli UDG come under Family I and are also called UNGs. The enzyme mechanism has been hotly debated. Classically, an acid/base mechanism has been employed (mechanism proposal 2), but new evidence suggests a steric distortion of the DNA substrate catalyses the reaction in a mechanism similar to SN1 dissociation (mechanism proposal 1).	Defined by 4 residues: ASP:A-64TYR:A-66PHE:A-77HIS:A-187 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.2.2.3 (PDB Primary Data) Search M-CSA Motif + EC 3.2.2.3

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.