1K82

Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped 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
Protein Modification Annotation
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)
I [auth A]	d1k82a1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Middle domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I [auth A]	d1k82a2	All beta proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I [auth A]	d1k82a3	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	C-terminal, Zn-finger domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J [auth B]	d1k82b1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Middle domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J [auth B]	d1k82b2	All beta proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J [auth B]	d1k82b3	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	C-terminal, Zn-finger domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K [auth C]	d1k82c1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Middle domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K [auth C]	d1k82c2	All beta proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K [auth C]	d1k82c3	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	C-terminal, Zn-finger domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L [auth D]	d1k82d1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Middle domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L [auth D]	d1k82d2	All beta proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	N-terminal domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L [auth D]	d1k82d3	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	C-terminal, Zn-finger domain of MutM-like DNA repair proteins	DNA repair protein MutM (Fpg)	(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)
I [auth A]	SCOP2 Family	Fpg (MutM)-like	8003736	4000303	SCOP2 (2022-06-29)
I [auth A]	SCOP2 Superfamily	S13-like H2TH domain	8003737	3000053	SCOP2 (2022-06-29)
I [auth A]	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8003740	3000068	SCOP2 (2022-06-29)
I [auth A]	SCOP2 Superfamily	FPG N-terminal domain-like	8056343	3000074	SCOP2 (2022-06-29)
J [auth B]	SCOP2B Superfamily	FPG N-terminal domain-like	8056343	3000074	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8003740	3000068	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	S13-like H2TH domain	8003737	3000053	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	S13-like H2TH domain	8003737	3000053	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8003740	3000068	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	FPG N-terminal domain-like	8056343	3000074	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	S13-like H2TH domain	8003737	3000053	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	FPG N-terminal domain-like	8056343	3000074	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8003740	3000068	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)
I [auth A]	Fapy_DNA_glyco	e1k82A1	A: beta barrels	X: MutM N-terminal domain-like	H: N-terminal domain of MutM-like DNA repair proteins (From Topology)	T: N-terminal domain of MutM-like DNA repair proteins	F: Fapy_DNA_glyco	ECOD (1.6)
I [auth A]	H2TH	e1k82A2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
I [auth A]	zf-FPG_IleRS	e1k82A3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: C-terminal, Zn-finger domain of MutM-like DNA repair proteins (From Topology)	T: C-terminal, Zn-finger domain of MutM-like DNA repair proteins	F: zf-FPG_IleRS	ECOD (1.6)
J [auth B]	Fapy_DNA_glyco	e1k82B1	A: beta barrels	X: MutM N-terminal domain-like	H: N-terminal domain of MutM-like DNA repair proteins (From Topology)	T: N-terminal domain of MutM-like DNA repair proteins	F: Fapy_DNA_glyco	ECOD (1.6)
J [auth B]	H2TH	e1k82B2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
J [auth B]	zf-FPG_IleRS	e1k82B3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: C-terminal, Zn-finger domain of MutM-like DNA repair proteins (From Topology)	T: C-terminal, Zn-finger domain of MutM-like DNA repair proteins	F: zf-FPG_IleRS	ECOD (1.6)
K [auth C]	Fapy_DNA_glyco	e1k82C1	A: beta barrels	X: MutM N-terminal domain-like	H: N-terminal domain of MutM-like DNA repair proteins (From Topology)	T: N-terminal domain of MutM-like DNA repair proteins	F: Fapy_DNA_glyco	ECOD (1.6)
K [auth C]	H2TH	e1k82C2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
K [auth C]	zf-FPG_IleRS	e1k82C3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: C-terminal, Zn-finger domain of MutM-like DNA repair proteins (From Topology)	T: C-terminal, Zn-finger domain of MutM-like DNA repair proteins	F: zf-FPG_IleRS	ECOD (1.6)
L [auth D]	Fapy_DNA_glyco	e1k82D1	A: beta barrels	X: MutM N-terminal domain-like	H: N-terminal domain of MutM-like DNA repair proteins (From Topology)	T: N-terminal domain of MutM-like DNA repair proteins	F: Fapy_DNA_glyco	ECOD (1.6)
L [auth D]	H2TH	e1k82D2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: H2TH	ECOD (1.6)
L [auth D]	zf-FPG_IleRS	e1k82D3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: C-terminal, Zn-finger domain of MutM-like DNA repair proteins (From Topology)	T: C-terminal, Zn-finger domain of MutM-like DNA repair proteins	F: zf-FPG_IleRS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth A]	3.20.190.10	Alpha Beta	Alpha-Beta Barrel	N-terminal domain of MutM-like DNA repair proteins	MutM-like, N-terminal	CATH (4.3.0)
I [auth A]	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
J [auth B]	3.20.190.10	Alpha Beta	Alpha-Beta Barrel	N-terminal domain of MutM-like DNA repair proteins	MutM-like, N-terminal	CATH (4.3.0)
J [auth B]	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
K [auth C]	3.20.190.10	Alpha Beta	Alpha-Beta Barrel	N-terminal domain of MutM-like DNA repair proteins	MutM-like, N-terminal	CATH (4.3.0)
K [auth C]	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
L [auth D]	3.20.190.10	Alpha Beta	Alpha-Beta Barrel	N-terminal domain of MutM-like DNA repair proteins	MutM-like, N-terminal	CATH (4.3.0)
L [auth D]	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth A], J [auth B], K [auth C], L [auth D]	PF06827	Zinc finger found in FPG and IleRS (zf-FPG_IleRS)	Zinc finger found in FPG and IleRS	This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	PF01149	Formamidopyrimidine-DNA glycosylase N-terminal domain (Fapy_DNA_glyco)	Formamidopyrimidine-DNA glycosylase N-terminal domain	Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges [1 ...	Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], C [auth F], E [auth G], G [auth H]	5'-D(GPGPCPTPTPCPCPTPCPCPTPGP*G)-3'	-	-	-
B [auth I], D [auth J], F [auth K], H [auth L]	5'-D(CPCPAPGPGPAP(PED)PGPAPAPGPCP*C)-3'	-	-	-
I [auth A], J [auth B], K [auth C], L [auth D]	formamidopyrimidine-DNA glycosylase	hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid oxidized purine nucleobase lesion DNA N-glycosylase activity hydrolase activity 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity DNA-(apurinic or apyrimidinic site) endonuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid oxidized purine nucleobase lesion DNA N-glycosylase activity hydrolase activity 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity DNA-(apurinic or apyrimidinic site) endonuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity carbon-oxygen lyase activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding damaged DNA binding nucleic acid binding	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 base-excision repair organic substance metabolic process 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 base-excision repair organic substance metabolic process metabolic process macromolecule metabolic process DNA repair	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth A], J [auth B], K [auth C], L [auth D]	IPR000214	Zinc finger, DNA glycosylase/AP lyase-type	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR035937	MutM-like, N-terminal	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR015887	DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site	Binding Site
I [auth A], J [auth B], K [auth C], L [auth D]	IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR020629	Formamidopyrimidine-DNA glycosylase	Family
I [auth A], J [auth B], K [auth C], L [auth D]	IPR015886	DNA glycosylase/AP lyase, H2TH DNA-binding	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR010663	Zinc finger, FPG/IleRS-type	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR010979	Small ribosomal subunit protein uS13-like, H2TH	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth I], D [auth J], F [auth K], H [auth L]	PED	RESID: AA0494 PSI-MOD : N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-prolinium MOD:01454

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

Chains	Enzyme Name	Description	Catalytic Residues
I [auth A]	DNA-formamidopyrimidine glycosylase M-CSA #659	Formamidopyrimidine-DNA glycosylase, otherwise known as Fpg or MutM, is a bifunctional base excision repair enzyme - it has both DNA glycosylase and AP lyase activities and is involved in removal of oxidised bases including 2,6-diamino-4-hydroxy- 5-formamidopyrimidine (FapydG) and 8-oxoguanine from oxidatively-damaged DNA in initiation of the base excision repair pathway.	Defined by 2 residues: PRO:I-1 [auth A-1]GLU:I-2 [auth A-2] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.2.2.23 (PDB Primary Data) Search M-CSA Motif + EC 3.2.2.23

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.