Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1K82

Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000703	molecular_function	oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003684	molecular_function	damaged DNA binding
A	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
A	0004519	molecular_function	endonuclease activity
A	0005737	cellular_component	cytoplasm
A	0006281	biological_process	DNA repair
A	0006284	biological_process	base-excision repair
A	0006974	biological_process	DNA damage response
A	0008270	molecular_function	zinc ion binding
A	0008534	molecular_function	oxidized purine nucleobase lesion DNA N-glycosylase activity
A	0016787	molecular_function	hydrolase activity
A	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
A	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
A	0016829	molecular_function	lyase activity
A	0019104	molecular_function	DNA N-glycosylase activity
A	0034039	molecular_function	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
A	0046872	molecular_function	metal ion binding
A	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
B	0000703	molecular_function	oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003684	molecular_function	damaged DNA binding
B	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
B	0004519	molecular_function	endonuclease activity
B	0005737	cellular_component	cytoplasm
B	0006281	biological_process	DNA repair
B	0006284	biological_process	base-excision repair
B	0006974	biological_process	DNA damage response
B	0008270	molecular_function	zinc ion binding
B	0008534	molecular_function	oxidized purine nucleobase lesion DNA N-glycosylase activity
B	0016787	molecular_function	hydrolase activity
B	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
B	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
B	0016829	molecular_function	lyase activity
B	0019104	molecular_function	DNA N-glycosylase activity
B	0034039	molecular_function	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
B	0046872	molecular_function	metal ion binding
B	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
C	0000703	molecular_function	oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
C	0003676	molecular_function	nucleic acid binding
C	0003677	molecular_function	DNA binding
C	0003684	molecular_function	damaged DNA binding
C	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
C	0004519	molecular_function	endonuclease activity
C	0005737	cellular_component	cytoplasm
C	0006281	biological_process	DNA repair
C	0006284	biological_process	base-excision repair
C	0006974	biological_process	DNA damage response
C	0008270	molecular_function	zinc ion binding
C	0008534	molecular_function	oxidized purine nucleobase lesion DNA N-glycosylase activity
C	0016787	molecular_function	hydrolase activity
C	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
C	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
C	0016829	molecular_function	lyase activity
C	0019104	molecular_function	DNA N-glycosylase activity
C	0034039	molecular_function	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
C	0046872	molecular_function	metal ion binding
C	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
D	0000703	molecular_function	oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
D	0003676	molecular_function	nucleic acid binding
D	0003677	molecular_function	DNA binding
D	0003684	molecular_function	damaged DNA binding
D	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
D	0004519	molecular_function	endonuclease activity
D	0005737	cellular_component	cytoplasm
D	0006281	biological_process	DNA repair
D	0006284	biological_process	base-excision repair
D	0006974	biological_process	DNA damage response
D	0008270	molecular_function	zinc ion binding
D	0008534	molecular_function	oxidized purine nucleobase lesion DNA N-glycosylase activity
D	0016787	molecular_function	hydrolase activity
D	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
D	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
D	0016829	molecular_function	lyase activity
D	0019104	molecular_function	DNA N-glycosylase activity
D	0034039	molecular_function	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
D	0046872	molecular_function	metal ion binding
D	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 450

Chain	Residue
A	CYS243
A	CYS246
A	CYS263
A	CYS266

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 450

Chain	Residue
B	CYS243
B	CYS246
B	CYS263
B	CYS266

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 450

Chain	Residue
C	CYS246
C	CYS263
C	CYS266
C	CYS243

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 450

Chain	Residue
D	CYS243
D	CYS246
D	CYS263
D	CYS266

Functional Information from PROSITE/UniProt

site_id	PS01242
Number of Residues	25
Details	ZF_FPG_1 Zinc finger FPG-type signature. Crv..CGtpIvatkhaq....RAtfYCrqCQ

Chain	Residue	Details
A	CYS243-GLN267

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	136
Details	ZN_FING: FPG-type

Chain	Residue	Details
A	GLN234-LYS268
B	GLN234-LYS268
C	GLN234-LYS268
D	GLN234-LYS268

site_id	SWS_FT_FI2
Number of Residues	4
Details	ACT_SITE: Schiff-base intermediate with DNA

Chain	Residue	Details
A	PRO1
B	PRO1
C	PRO1
D	PRO1

site_id	SWS_FT_FI3
Number of Residues	4
Details	ACT_SITE: Proton donor => ECO:0000305

Chain	Residue	Details
A	GLU2
B	GLU2
C	GLU2
D	GLU2

site_id	SWS_FT_FI4
Number of Residues	4
Details	ACT_SITE: Proton donor; for beta-elimination activity => ECO:0000305

Chain	Residue	Details
A	LYS56
B	LYS56
C	LYS56
D	LYS56

site_id	SWS_FT_FI5
Number of Residues	4
Details	ACT_SITE: Proton donor; for delta-elimination activity => ECO:0000305

Chain	Residue	Details
A	ARG258
B	ARG258
C	ARG258
D	ARG258

site_id	SWS_FT_FI6
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:11912217

Chain	Residue	Details
A	HIS89
D	HIS89
D	ARG108
D	LYS149
A	ARG108
A	LYS149
B	HIS89
B	ARG108
B	LYS149
C	HIS89
C	ARG108
C	LYS149

Catalytic Information from CSA

site_id	CSA1
Number of Residues	4
Details	a catalytic site defined by CSA, PubMed 10921868, 11912217, 9030608, 12065399, 11106507, 9826758

Chain	Residue	Details
A	GLU2
A	LYS56
A	PRO1
A	ARG258

site_id	CSA2
Number of Residues	4
Details	a catalytic site defined by CSA, PubMed 10921868, 11912217, 9030608, 12065399, 11106507, 9826758

Chain	Residue	Details
B	GLU2
B	LYS56
B	PRO1
B	ARG258

site_id	CSA3
Number of Residues	4
Details	a catalytic site defined by CSA, PubMed 10921868, 11912217, 9030608, 12065399, 11106507, 9826758

Chain	Residue	Details
C	GLU2
C	LYS56
C	PRO1
C	ARG258

site_id	CSA4
Number of Residues	4
Details	a catalytic site defined by CSA, PubMed 10921868, 11912217, 9030608, 12065399, 11106507, 9826758

Chain	Residue	Details
D	GLU2
D	LYS56
D	PRO1
D	ARG258

site_id	MCSA1
Number of Residues	2
Details	M-CSA 659

Chain	Residue	Details
A	PRO1	covalently attached, electron pair donor, nucleophile, proton donor
A	GLU2	proton acceptor, proton donor

site_id	MCSA2
Number of Residues	2
Details	M-CSA 659

Chain	Residue	Details
B	PRO1	covalently attached, electron pair donor, nucleophile, proton donor
B	GLU2	proton acceptor, proton donor

site_id	MCSA3
Number of Residues	2
Details	M-CSA 659

Chain	Residue	Details
C	PRO1	covalently attached, electron pair donor, nucleophile, proton donor
C	GLU2	proton acceptor, proton donor

site_id	MCSA4
Number of Residues	2
Details	M-CSA 659

Chain	Residue	Details
D	PRO1	covalently attached, electron pair donor, nucleophile, proton donor
D	GLU2	proton acceptor, proton donor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)