1EUG | pdb_00001eug

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-e 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 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	cellular anatomical structure intracellular anatomical structure cytoplasm

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 EC: 3.2.2.27 (UniProt) Search M-CSA Motif + EC 3.2.2.27

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.