DNA-glycosylase superfamily

SCOP classification

Root:	SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:	All alpha proteins [ 46456] (284)
Fold:	DNA-glycosylase [ 48149]
Superfamily:	DNA-glycosylase [ 48150] (6)
Families:	Endonuclease III [ 48151]
	Mismatch glycosylase [ 48154] (3)
	3-Methyladenine DNA glycosylase I (Tag) [ 74756]
	3-Methyladenine DNA glycosylase III (MagIII) [ 101349]
	DNA repair glycosylase, 2 C-terminal domains [ 48157] (2)
	AgoG-like [ 116976] (2)

Superfamily statistics

	Genomes (2,420)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	10,175	28,720	36
Proteins	10,144	28,687	36

Functional annotation

General category	Information
Detailed category	DNA replication/repair

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)

	GO term	FDR (singleton)	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	cellular aromatic compound metabolic process	3.539e-09	0	Least Informative	Direct
Biological Process (BP)	nitrogen compound metabolic process	1.057e-07	0	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	4.564e-08	0	Least Informative	Direct
Biological Process (BP)	single-organism cellular process	6.884e-05	0.0001798	Least Informative	Direct
Biological Process (BP)	heterocycle metabolic process	2.927e-09	0	Least Informative	Direct
Biological Process (BP)	response to stimulus	1.249e-05	3.086e-11	Least Informative	Direct
Biological Process (BP)	organic cyclic compound metabolic process	1.321e-08	0	Least Informative	Direct
Biological Process (BP)	cellular response to stress	9.05e-15	0	Moderately Informative	Direct
Biological Process (BP)	DNA metabolic process	0	0	Informative	Direct
Biological Process (BP)	response to DNA damage stimulus	0	0	Informative	Direct
Biological Process (BP)	DNA repair	1.21e-06	5.386e-11	Highly Informative	Direct
Molecular Function (MF)	hydrolase activity	0.0007131	7.973e-16	Least Informative	Direct
Molecular Function (MF)	lyase activity	0.0008783	1.111e-14	Moderately Informative	Direct
Molecular Function (MF)	hydrolase activity, acting on glycosyl bonds	6.298e-15	0	Informative	Direct
Molecular Function (MF)	carbon-oxygen lyase activity	1.521e-06	0	Informative	Direct
Molecular Function (MF)	hydrolase activity, hydrolyzing N-glycosyl compounds	0	0	Highly Informative	Direct

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)

	GO term	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	cellular aromatic compound metabolic process	0	Least Informative	Direct
Biological Process (BP)	nitrogen compound metabolic process	0	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	0	Least Informative	Direct
Biological Process (BP)	single-organism cellular process	0.0001798	Least Informative	Direct
Biological Process (BP)	heterocycle metabolic process	0	Least Informative	Direct
Biological Process (BP)	response to stimulus	3.086e-11	Least Informative	Direct
Biological Process (BP)	organic cyclic compound metabolic process	0	Least Informative	Direct
Biological Process (BP)	single-organism metabolic process	1	Least Informative	Inherited
Biological Process (BP)	regulation of metabolic process	0.3077	Least Informative	Inherited
Biological Process (BP)	cellular response to stress	0	Moderately Informative	Direct
Biological Process (BP)	organic substance catabolic process	0.4474	Moderately Informative	Inherited
Biological Process (BP)	organophosphate metabolic process	0.5361	Moderately Informative	Inherited
Biological Process (BP)	carbohydrate derivative metabolic process	0.6254	Moderately Informative	Inherited
Biological Process (BP)	phosphate-containing compound metabolic process	0.256	Moderately Informative	Inherited
Biological Process (BP)	nucleobase-containing small molecule metabolic process	0.9458	Moderately Informative	Inherited
Biological Process (BP)	cellular catabolic process	0.277	Moderately Informative	Inherited
Biological Process (BP)	regulation of gene expression	0.05577	Moderately Informative	Inherited
Biological Process (BP)	DNA metabolic process	0	Informative	Direct
Biological Process (BP)	response to DNA damage stimulus	0	Informative	Direct
Biological Process (BP)	organophosphate catabolic process	0.000323	Informative	Direct
Biological Process (BP)	carbohydrate derivative catabolic process	0.0007571	Informative	Direct
Biological Process (BP)	nucleobase-containing compound catabolic process	0.1838	Informative	Inherited
Biological Process (BP)	cellular macromolecule catabolic process	0.003601	Informative	Inherited
Biological Process (BP)	DNA repair	5.386e-11	Highly Informative	Direct
Biological Process (BP)	DNA catabolic process	4.169e-08	Highly Informative	Direct
Biological Process (BP)	nucleotide catabolic process	1.02e-05	Highly Informative	Direct
Biological Process (BP)	deoxyribonucleotide metabolic process	4.463e-12	Highly Informative	Direct
Biological Process (BP)	deoxyribose phosphate metabolic process	2.452e-13	Highly Informative	Direct
Biological Process (BP)	regulation of gene expression, epigenetic	2.635e-12	Highly Informative	Direct
Biological Process (BP)	DNA methylation or demethylation	1	Highly Informative	Inherited
Molecular Function (MF)	hydrolase activity	7.973e-16	Least Informative	Direct
Molecular Function (MF)	lyase activity	1.111e-14	Moderately Informative	Direct
Molecular Function (MF)	hydrolase activity, acting on glycosyl bonds	0	Informative	Direct
Molecular Function (MF)	carbon-oxygen lyase activity	0	Informative	Direct
Molecular Function (MF)	hydrolase activity, hydrolyzing N-glycosyl compounds	0	Highly Informative	Direct
Cellular Component (CC)	intracellular membrane-bounded organelle	1.222e-07	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	0.704	Least Informative	Inherited
Cellular Component (CC)	intracellular non-membrane-bounded organelle	0.6572	Least Informative	Inherited
Cellular Component (CC)	intracellular organelle lumen	0.0006816	Moderately Informative	Direct
Cellular Component (CC)	nuclear part	0.5046	Moderately Informative	Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Lyases	0	Least Informative	Direct
Enzyme Commission (EC)	Other carbon-oxygen lyases	0	Informative	Direct
Enzyme Commission (EC)	Hydrolyzing N-glycosyl compounds	6.815e-12	Informative	Direct
Enzyme Commission (EC)	DNA-(apurinic or apyrimidinic site) lyase	0	Highly Informative	Direct

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)

	MP term	FDR (all)	SDMP level	Annotation (direct or inherited)
Mammalian Phenotype (MP)	cellular phenotype	0	Least Informative	Direct
Mammalian Phenotype (MP)	tumorigenesis	0.002646	Moderately Informative	Inherited
Mammalian Phenotype (MP)	abnormal metabolism	0.008102	Informative	Inherited
Mammalian Phenotype (MP)	increased adenoma incidence	9.866e-06	Highly Informative	Direct
Mammalian Phenotype (MP)	abnormal DNA repair	2.274e-05	Highly Informative	Direct
Mammalian Phenotype (MP)	decreased physiological sensitivity to xenobiotic	7.085e-05	Highly Informative	Direct

Document: MP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)

	XA term	FDR (all)	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	head	0	Least Informative	Direct

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)

	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	stem	0	Least Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Lyases	0	Least Informative	Direct
Enzyme Commission (EC)	Hydrolases	1	Least Informative	Inherited
Enzyme Commission (EC)	Carbon-oxygen lyases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Glycosylases	1.982e-06	Moderately Informative	Direct
Enzyme Commission (EC)	DNA-(apurinic or apyrimidinic site) lyase	0	Highly Informative	Direct
Enzyme Commission (EC)	Hydrolyzing N-glycosyl compounds	7.95e-12	Highly Informative	Direct

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	DNA damage	0	Moderately Informative	Direct
Biological process	DNA excision	1.426e-11	Highly Informative	Direct
Cellular component	Nucleus	3.22e-06	Least Informative	Direct
Molecular function	Metal-binding	5.73e-11	Least Informative	Direct
Molecular function	Iron	0	Moderately Informative	Direct
Molecular function	DNA-binding	7.15e-11	Moderately Informative	Direct
Molecular function	4Fe-4S	0	Informative	Direct
Molecular function	Iron-sulfur	0	Informative	Direct
Post-translational modification	Hydrolase	0	Least Informative	Direct
Post-translational modification	Lyase	0	Moderately Informative	Direct
Post-translational modification	Glycosidase	0	Informative	Direct

Document: KW annotation of SCOP domains

InterPro annotation

Cross references IPR011257 SSF48150 Protein matches

Abstract
DNA glycosylases act to repair oxidative damage in DNA. These proteins are redundant as there are several different types of DNA glycosylases that are ale to compensate for one another. Examples include the endonuclease III subfamily, the mismatch glycosylases subfamily, the 3-methyladenine DNA glycosylases I subfamily, and the DNA repair glycosylases subfamily [ PubMed 14637253].

InterPro database

PDBeMotif information about ligands, sequence and structure motifs

Cross references

PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 12 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.

Browse and view proteins in genomes which have different domain combinations including a DNA-glycosylase domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.

Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 12 hidden Markov models representing the DNA-glycosylase superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

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DNA-glycosylase superfamily