Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4IEM

Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000723	biological_process	telomere maintenance
A	0000781	cellular_component	chromosome, telomeric region
A	0003677	molecular_function	DNA binding
A	0003684	molecular_function	damaged DNA binding
A	0003691	molecular_function	double-stranded telomeric DNA binding
A	0003713	molecular_function	transcription coactivator activity
A	0003714	molecular_function	transcription corepressor activity
A	0003723	molecular_function	RNA binding
A	0003824	molecular_function	catalytic activity
A	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
A	0004518	molecular_function	nuclease activity
A	0004519	molecular_function	endonuclease activity
A	0004520	molecular_function	DNA endonuclease activity
A	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
A	0004527	molecular_function	exonuclease activity
A	0004528	molecular_function	phosphodiesterase I activity
A	0004844	molecular_function	uracil DNA N-glycosylase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005730	cellular_component	nucleolus
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005783	cellular_component	endoplasmic reticulum
A	0005813	cellular_component	centrosome
A	0005840	cellular_component	ribosome
A	0006281	biological_process	DNA repair
A	0006284	biological_process	base-excision repair
A	0006287	biological_process	base-excision repair, gap-filling
A	0006308	biological_process	DNA catabolic process
A	0006310	biological_process	DNA recombination
A	0006974	biological_process	DNA damage response
A	0008081	molecular_function	phosphoric diester hydrolase activity
A	0008296	molecular_function	3'-5'-DNA exonuclease activity
A	0008309	molecular_function	double-stranded DNA exodeoxyribonuclease activity
A	0008311	molecular_function	double-stranded DNA 3'-5' DNA exonuclease activity
A	0008408	molecular_function	3'-5' exonuclease activity
A	0016491	molecular_function	oxidoreductase activity
A	0016607	cellular_component	nuclear speck
A	0016787	molecular_function	hydrolase activity
A	0031490	molecular_function	chromatin DNA binding
A	0033892	molecular_function	deoxyribonuclease (pyrimidine dimer) activity
A	0042981	biological_process	regulation of apoptotic process
A	0043488	biological_process	regulation of mRNA stability
A	0044029	biological_process	positive regulation of gene expression via chromosomal CpG island demethylation
A	0045454	biological_process	cell redox homeostasis
A	0045892	biological_process	negative regulation of DNA-templated transcription
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
A	0048471	cellular_component	perinuclear region of cytoplasm
A	0052720	molecular_function	class II DNA-(apurinic or apyrimidinic site) endonuclease activity
A	0090580	molecular_function	phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
A	0097698	biological_process	telomere maintenance via base-excision repair
A	0140431	molecular_function	DNA-(abasic site) binding
B	0000723	biological_process	telomere maintenance
B	0000781	cellular_component	chromosome, telomeric region
B	0003677	molecular_function	DNA binding
B	0003684	molecular_function	damaged DNA binding
B	0003691	molecular_function	double-stranded telomeric DNA binding
B	0003713	molecular_function	transcription coactivator activity
B	0003714	molecular_function	transcription corepressor activity
B	0003723	molecular_function	RNA binding
B	0003824	molecular_function	catalytic activity
B	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
B	0004518	molecular_function	nuclease activity
B	0004519	molecular_function	endonuclease activity
B	0004520	molecular_function	DNA endonuclease activity
B	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
B	0004527	molecular_function	exonuclease activity
B	0004528	molecular_function	phosphodiesterase I activity
B	0004844	molecular_function	uracil DNA N-glycosylase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005730	cellular_component	nucleolus
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005783	cellular_component	endoplasmic reticulum
B	0005813	cellular_component	centrosome
B	0005840	cellular_component	ribosome
B	0006281	biological_process	DNA repair
B	0006284	biological_process	base-excision repair
B	0006287	biological_process	base-excision repair, gap-filling
B	0006308	biological_process	DNA catabolic process
B	0006310	biological_process	DNA recombination
B	0006974	biological_process	DNA damage response
B	0008081	molecular_function	phosphoric diester hydrolase activity
B	0008296	molecular_function	3'-5'-DNA exonuclease activity
B	0008309	molecular_function	double-stranded DNA exodeoxyribonuclease activity
B	0008311	molecular_function	double-stranded DNA 3'-5' DNA exonuclease activity
B	0008408	molecular_function	3'-5' exonuclease activity
B	0016491	molecular_function	oxidoreductase activity
B	0016607	cellular_component	nuclear speck
B	0016787	molecular_function	hydrolase activity
B	0031490	molecular_function	chromatin DNA binding
B	0033892	molecular_function	deoxyribonuclease (pyrimidine dimer) activity
B	0042981	biological_process	regulation of apoptotic process
B	0043488	biological_process	regulation of mRNA stability
B	0044029	biological_process	positive regulation of gene expression via chromosomal CpG island demethylation
B	0045454	biological_process	cell redox homeostasis
B	0045892	biological_process	negative regulation of DNA-templated transcription
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0046872	molecular_function	metal ion binding
B	0048471	cellular_component	perinuclear region of cytoplasm
B	0052720	molecular_function	class II DNA-(apurinic or apyrimidinic site) endonuclease activity
B	0090580	molecular_function	phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
B	0097698	biological_process	telomere maintenance via base-excision repair
B	0140431	molecular_function	DNA-(abasic site) binding
C	0000723	biological_process	telomere maintenance
C	0000781	cellular_component	chromosome, telomeric region
C	0003677	molecular_function	DNA binding
C	0003684	molecular_function	damaged DNA binding
C	0003691	molecular_function	double-stranded telomeric DNA binding
C	0003713	molecular_function	transcription coactivator activity
C	0003714	molecular_function	transcription corepressor activity
C	0003723	molecular_function	RNA binding
C	0003824	molecular_function	catalytic activity
C	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
C	0004518	molecular_function	nuclease activity
C	0004519	molecular_function	endonuclease activity
C	0004520	molecular_function	DNA endonuclease activity
C	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
C	0004527	molecular_function	exonuclease activity
C	0004528	molecular_function	phosphodiesterase I activity
C	0004844	molecular_function	uracil DNA N-glycosylase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005730	cellular_component	nucleolus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005783	cellular_component	endoplasmic reticulum
C	0005813	cellular_component	centrosome
C	0005840	cellular_component	ribosome
C	0006281	biological_process	DNA repair
C	0006284	biological_process	base-excision repair
C	0006287	biological_process	base-excision repair, gap-filling
C	0006308	biological_process	DNA catabolic process
C	0006310	biological_process	DNA recombination
C	0006974	biological_process	DNA damage response
C	0008081	molecular_function	phosphoric diester hydrolase activity
C	0008296	molecular_function	3'-5'-DNA exonuclease activity
C	0008309	molecular_function	double-stranded DNA exodeoxyribonuclease activity
C	0008311	molecular_function	double-stranded DNA 3'-5' DNA exonuclease activity
C	0008408	molecular_function	3'-5' exonuclease activity
C	0016491	molecular_function	oxidoreductase activity
C	0016607	cellular_component	nuclear speck
C	0016787	molecular_function	hydrolase activity
C	0031490	molecular_function	chromatin DNA binding
C	0033892	molecular_function	deoxyribonuclease (pyrimidine dimer) activity
C	0042981	biological_process	regulation of apoptotic process
C	0043488	biological_process	regulation of mRNA stability
C	0044029	biological_process	positive regulation of gene expression via chromosomal CpG island demethylation
C	0045454	biological_process	cell redox homeostasis
C	0045892	biological_process	negative regulation of DNA-templated transcription
C	0045944	biological_process	positive regulation of transcription by RNA polymerase II
C	0046872	molecular_function	metal ion binding
C	0048471	cellular_component	perinuclear region of cytoplasm
C	0052720	molecular_function	class II DNA-(apurinic or apyrimidinic site) endonuclease activity
C	0090580	molecular_function	phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
C	0097698	biological_process	telomere maintenance via base-excision repair
C	0140431	molecular_function	DNA-(abasic site) binding
D	0000723	biological_process	telomere maintenance
D	0000781	cellular_component	chromosome, telomeric region
D	0003677	molecular_function	DNA binding
D	0003684	molecular_function	damaged DNA binding
D	0003691	molecular_function	double-stranded telomeric DNA binding
D	0003713	molecular_function	transcription coactivator activity
D	0003714	molecular_function	transcription corepressor activity
D	0003723	molecular_function	RNA binding
D	0003824	molecular_function	catalytic activity
D	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
D	0004518	molecular_function	nuclease activity
D	0004519	molecular_function	endonuclease activity
D	0004520	molecular_function	DNA endonuclease activity
D	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
D	0004527	molecular_function	exonuclease activity
D	0004528	molecular_function	phosphodiesterase I activity
D	0004844	molecular_function	uracil DNA N-glycosylase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005730	cellular_component	nucleolus
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005783	cellular_component	endoplasmic reticulum
D	0005813	cellular_component	centrosome
D	0005840	cellular_component	ribosome
D	0006281	biological_process	DNA repair
D	0006284	biological_process	base-excision repair
D	0006287	biological_process	base-excision repair, gap-filling
D	0006308	biological_process	DNA catabolic process
D	0006310	biological_process	DNA recombination
D	0006974	biological_process	DNA damage response
D	0008081	molecular_function	phosphoric diester hydrolase activity
D	0008296	molecular_function	3'-5'-DNA exonuclease activity
D	0008309	molecular_function	double-stranded DNA exodeoxyribonuclease activity
D	0008311	molecular_function	double-stranded DNA 3'-5' DNA exonuclease activity
D	0008408	molecular_function	3'-5' exonuclease activity
D	0016491	molecular_function	oxidoreductase activity
D	0016607	cellular_component	nuclear speck
D	0016787	molecular_function	hydrolase activity
D	0031490	molecular_function	chromatin DNA binding
D	0033892	molecular_function	deoxyribonuclease (pyrimidine dimer) activity
D	0042981	biological_process	regulation of apoptotic process
D	0043488	biological_process	regulation of mRNA stability
D	0044029	biological_process	positive regulation of gene expression via chromosomal CpG island demethylation
D	0045454	biological_process	cell redox homeostasis
D	0045892	biological_process	negative regulation of DNA-templated transcription
D	0045944	biological_process	positive regulation of transcription by RNA polymerase II
D	0046872	molecular_function	metal ion binding
D	0048471	cellular_component	perinuclear region of cytoplasm
D	0052720	molecular_function	class II DNA-(apurinic or apyrimidinic site) endonuclease activity
D	0090580	molecular_function	phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
D	0097698	biological_process	telomere maintenance via base-excision repair
D	0140431	molecular_function	DNA-(abasic site) binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 501

Chain	Residue
A	HOH641
E	DC505
G	DG518
G	DT519
G	HOH606

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 502

Chain	Residue
E	DC505
F	3DR506
A	GLU96
A	HOH601
A	HOH602
A	HOH603

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG A 503

Chain	Residue
L	DT509
M	DT515

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA A 504

Chain	Residue
A	TYR269
A	MET270
A	MET271
A	ASN272
G	DG518

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA A 505

Chain	Residue
A	LEU44
A	TYR45

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 401

Chain	Residue
B	GLU96
B	HOH502
B	HOH503
H	DC505
I	3DR506
I	HOH601

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA B 402

Chain	Residue
B	ASP47
B	TYR257
B	SER298
B	LYS299

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA B 403

Chain	Residue
B	ARG185
B	ASP189
B	VAL213
B	GLU236

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA B 404

Chain	Residue
B	ASP189
B	ARG193
B	LEU243

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 401

Chain	Residue
C	GLU96
C	HOH601
C	HOH602
K	DC505
K	HOH701
L	3DR506

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG C 402

Chain	Residue
C	ASP70
C	HOH614
C	HOH668
K	DC505
K	HOH701
M	DG518
M	DT519

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 401

Chain	Residue
D	GLU96
D	HOH501
D	HOH502
N	DC505
N	HOH701
O	3DR506

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA D 402

Chain	Residue
D	ASN222
O	DT509

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA E 601

Chain	Residue
E	DT503
E	DA504

site_id	BC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NA F 601

Chain	Residue
F	DC510

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA N 601

Chain	Residue
N	DT503
N	DA504

Functional Information from PROSITE/UniProt

site_id	PS00726
Number of Residues	10
Details	AP_NUCLEASE_F1_1 AP endonucleases family 1 signature 1. PDILCLQETK

Chain	Residue	Details
A	PRO89-LYS98

site_id	PS00727
Number of Residues	17
Details	AP_NUCLEASE_F1_2 AP endonucleases family 1 signature 2. DSFRHlypntpyaYTFW

Chain	Residue	Details
A	ASP251-TRP267

site_id	PS00728
Number of Residues	12
Details	AP_NUCLEASE_F1_3 AP endonucleases family 1 signature 3. NvGwRLDYfLlS

Chain	Residue	Details
A	ASN277-SER288

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: ACT_SITE => ECO:0000269\|PubMed:15380100

Chain	Residue	Details
A	TYR171
B	TYR171
C	TYR171
D	TYR171

site_id	SWS_FT_FI2
Number of Residues	4
Details	ACT_SITE: Proton donor/acceptor => ECO:0000269\|PubMed:9351835, ECO:0007744\|PDB:1BIX

Chain	Residue	Details
A	ASP210
B	ASP210
C	ASP210
D	ASP210

site_id	SWS_FT_FI3
Number of Residues	4
Details	ACT_SITE: Proton acceptor => ECO:0000255\|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	HIS309
B	HIS309
C	HIS309
D	HIS309

site_id	SWS_FT_FI4
Number of Residues	24
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	ASN68
B	ASN212
B	ASP308
B	HIS309
C	ASN68
C	GLU96
C	ASP210
C	ASN212
C	ASP308
C	HIS309
D	ASN68
A	GLU96
D	GLU96
D	ASP210
D	ASN212
D	ASP308
D	HIS309
A	ASP210
A	ASN212
A	ASP308
A	HIS309
B	ASN68
B	GLU96
B	ASP210

site_id	SWS_FT_FI5
Number of Residues	4
Details	SITE: Cleavage; by granzyme A

Chain	Residue	Details
A	LYS31
B	LYS31
C	LYS31
D	LYS31

site_id	SWS_FT_FI6
Number of Residues	4
Details	SITE: Transition state stabilizer => ECO:0000269\|PubMed:8932375

Chain	Residue	Details
A	ASN212
B	ASN212
C	ASN212
D	ASN212

site_id	SWS_FT_FI7
Number of Residues	4
Details	SITE: Important for catalytic activity => ECO:0000269\|PubMed:21762700, ECO:0000269\|PubMed:9804799

Chain	Residue	Details
A	ASP283
B	ASP283
C	ASP283
D	ASP283

site_id	SWS_FT_FI8
Number of Residues	4
Details	SITE: Interaction with DNA substrate

Chain	Residue	Details
A	HIS309
B	HIS309
C	HIS309
D	HIS309

site_id	SWS_FT_FI9
Number of Residues	8
Details	MOD_RES: N6-acetyllysine; by EP300 => ECO:0000269\|PubMed:14633989

Chain	Residue	Details
A	LYS6
A	LYS7
B	LYS6
B	LYS7
C	LYS6
C	LYS7
D	LYS6
D	LYS7

site_id	SWS_FT_FI10
Number of Residues	16
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:20699270

Chain	Residue	Details
A	LYS27
C	LYS31
C	LYS32
C	LYS35
D	LYS27
D	LYS31
D	LYS32
D	LYS35
A	LYS31
A	LYS32
A	LYS35
B	LYS27
B	LYS31
B	LYS32
B	LYS35
C	LYS27

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER54
B	SER54
C	SER54
D	SER54

site_id	SWS_FT_FI12
Number of Residues	8
Details	MOD_RES: S-nitrosocysteine; alternate => ECO:0000269\|PubMed:17403694

Chain	Residue	Details
A	CYS65
A	CYS93
B	CYS65
B	CYS93
C	CYS65
C	CYS93
D	CYS65
D	CYS93

site_id	SWS_FT_FI13
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	LYS197
B	LYS197
C	LYS197
D	LYS197

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: Phosphothreonine; by CDK5 => ECO:0000250\|UniProtKB:P28352

Chain	Residue	Details
A	THR233
B	THR233
C	THR233
D	THR233

site_id	SWS_FT_FI15
Number of Residues	4
Details	MOD_RES: S-nitrosocysteine => ECO:0000269\|PubMed:17403694

Chain	Residue	Details
A	CYS310
B	CYS310
C	CYS310
D	CYS310

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
A	ASP70	metal ligand
A	GLU96	metal ligand
A	TYR171	electrostatic stabiliser, metal ligand
A	ASP210	increase nucleophilicity, metal ligand, proton acceptor
A	ASN212
A	ASP283	electrostatic stabiliser
A	ASP308	metal ligand
A	HIS309	electrostatic stabiliser, metal ligand

site_id	MCSA2
Number of Residues	8
Details	M-CSA 510

Chain

Residue

Details

site_id	MCSA3
Number of Residues	8
Details	M-CSA 510

Chain

Residue

Details

site_id	MCSA4
Number of Residues	8
Details	M-CSA 510

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)