1DIZ

CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA

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)
E [auth A]	d1diza1	All alpha proteins	DNA-glycosylase	DNA-glycosylase	DNA repair glycosylase, 2 C-terminal domains	3-Methyladenine DNA glycosylase II (gene alkA or aidA)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth A]	d1diza2	Alpha and beta proteins (a+b)	TBP-like	TATA-box binding protein-like	DNA repair glycosylase, N-terminal domain	3-Methyladenine DNA glycosylase II (gene alkA or aidA)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth B]	d1dizb1	All alpha proteins	DNA-glycosylase	DNA-glycosylase	DNA repair glycosylase, 2 C-terminal domains	3-Methyladenine DNA glycosylase II (gene alkA or aidA)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth B]	d1dizb2	Alpha and beta proteins (a+b)	TBP-like	TATA-box binding protein-like	DNA repair glycosylase, N-terminal domain	3-Methyladenine DNA glycosylase II (gene alkA or aidA)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2B Superfamily	DNA-glycosylase	8038321	3000905	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	TATA-box binding protein-like	8036364	3000705	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	TATA-box binding protein-like	8036364	3000705	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	DNA-glycosylase	8038321	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)
E [auth A]	HhH-GPD	e1dizA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD	ECOD (1.6)
E [auth A]	AlkA_N	e1dizA2	A: a+b two layers	X: TBP-like	H: TATA-box binding protein-like (From Topology)	T: TATA-box binding protein-like	F: AlkA_N	ECOD (1.6)
F [auth B]	HhH-GPD	e1dizB1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: HhH-GPD	ECOD (1.6)
F [auth B]	AlkA_N	e1dizB2	A: a+b two layers	X: TBP-like	H: TATA-box binding protein-like (From Topology)	T: TATA-box binding protein-like	F: AlkA_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth A]	3.30.310.20	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	DNA-3-methyladenine glycosylase AlkA, N-terminal domain	CATH (4.3.0)
E [auth A]	1.10.340.30	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)
E [auth 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)
F [auth B]	3.30.310.20	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	DNA-3-methyladenine glycosylase AlkA, N-terminal domain	CATH (4.3.0)
F [auth B]	1.10.340.30	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)
F [auth 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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B]	PF06029	AlkA N-terminal domain (AlkA_N)	AlkA N-terminal domain	-	Domain
E [auth A], F [auth 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 [auth C], C [auth E]	DNA (5'-D(GPAPCPAPTPGPAP(NRI)PTPGPCPCP*T)-3')	-	-	-
B [auth D], D [auth F]	DNA (5'-D(GPGPCPAPAPTPCPAPTPGPTPCP*A)-3')	-	-	-
E [auth A], F [auth B]	3-METHYLADENINE DNA GLYCOSYLASE II	alkylbase DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds 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 DNA-3-methylguanine glycosylase activity DNA-3-methylbase glycosylase activity DNA binding alkylated DNA binding binding organic cyclic compound binding alkylbase DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds 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 DNA-3-methylguanine glycosylase activity DNA-3-methylbase glycosylase activity DNA binding alkylated DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid binding DNA-3-methyladenine glycosylase activity DNA-7-methyladenine glycosylase activity DNA-7-methylguanine glycosylase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process macromolecule metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process macromolecule metabolic process DNA repair base-excision repair DNA alkylation repair base-excision repair, AP site formation	protein-containing complex protein-DNA complex intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR000035	Alkylbase DNA glycosidase, conserved site	Conserved Site
E [auth A], F [auth B]	IPR003265	HhH-GPD domain	Domain
E [auth A], F [auth B]	IPR023170	Helix-hairpin-helix, base-excision DNA repair, C-terminal	Homologous Superfamily
E [auth A], F [auth B]	IPR037046	DNA-3-methyladenine glycosylase AlkA, N-terminal domain superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR010316	DNA-3-methyladenine glycosylase AlkA, N-terminal	Domain
E [auth A], F [auth B]	IPR011257	DNA glycosylase	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
E [auth A]	DNA-3-methyladenine glycosylase II M-CSA #313	A variety of environmental toxins can react with DNA and chemically alkylate the bases. This blocks the replicative polymerases and interferes with binding of regulatory proteins to DNA resulting in widespread cellular responses including activation of cell cycle checkpoints and programmed cell death. There are a number of repair strategies - direct reversal, nucleotide excision repair and base excision repair. Most single base modifications are corrected using base excision repair. Firstly a lesion specific DNA glycosylase removes the damaged base by hydrolysis of the deoxyribose glycosidic bond of alkylated DNA. The abasic site is then excised and filled by DNA polymerase. AlkA lacks an obvious residue that could fulfill the role of a general acid to protonate the leaving group and later activate a water molecule. It is thought that AlkA's positively charged, alkylated substrates might not require this type of assistance. The lack of a general acid in AlkA's active site provides a means of catalytic selectivity. Positively charged bases, which do not require protonation and have a weakened glycosylic bond, can be removed effectively, and in turn it may function as a general base to activate a nearby water molecule. Unmodified bases require protonation by a general acid prior to hydrolysis and therefore are poor substrates. [PMID:10675345]	Defined by 3 residues: TRP:E-218 [auth A-218]TYR:E-222 [auth A-222]ASP:E-238 [auth A-238] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.2.2.21 (PDB Primary Data) Search M-CSA Motif + EC 3.2.2.21

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.