1PU8

Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) bound to 1,N6-ethenoadenine

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

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1pu8b_	All alpha proteins	DNA-glycosylase	DNA-glycosylase	3-Methyladenine DNA glycosylase III (MagIII)	3-Methyladenine DNA glycosylase III (MagIII)	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
A	d1pu8a_	All alpha proteins	DNA-glycosylase	DNA-glycosylase	3-Methyladenine DNA glycosylase III (MagIII)	3-Methyladenine DNA glycosylase III (MagIII)	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	DNA-glycosylase	8039091	3000905	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA-glycosylase	8039091	3000905	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)
B	HhH-GPD	e1pu8B1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD	ECOD (1.6)
A	HhH-GPD	e1pu8A1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.1670.10	Mainly Alpha	Orthogonal Bundle	Endonuclease Iii, domain 2	Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)	CATH (4.3.0)
B	1.10.340.30	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)
A	1.10.1670.10	Mainly Alpha	Orthogonal Bundle	Endonuclease Iii, domain 2	Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)	CATH (4.3.0)
A	1.10.340.30	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00730	HhH-GPD superfamily base excision DNA repair protein (HhH-GPD)	HhH-GPD superfamily base excision DNA repair protein	This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonucle ...	This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases such as Swiss:P53397. The methyl-CPG binding protein MBD4 Swiss:Q9Z2D7 also contains a related domain [1] that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	3-METHYLADENINE DNA GLYCOSYLASE	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	cellular response to stimulus response to stimulus cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process base-excision repair organic substance metabolic process heterocycle metabolic process cellular response to stress DNA damage response response to stress cellular response to stimulus response to stimulus cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process base-excision repair organic substance metabolic process heterocycle metabolic process cellular response to stress DNA damage response response to stress nitrogen compound metabolic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003265	HhH-GPD domain	Domain
A, B	IPR023170	Helix-hairpin-helix, base-excision DNA repair, C-terminal	Homologous Superfamily
A, B	IPR011257	DNA glycosylase	Homologous Superfamily

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.