7LPI

APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0003677	molecular_function	DNA binding
B	0003824	molecular_function	catalytic activity
B	0004518	molecular_function	nuclease activity
B	0004519	molecular_function	endonuclease activity
B	0006281	biological_process	DNA repair
D	0003677	molecular_function	DNA binding
D	0003824	molecular_function	catalytic activity
D	0004518	molecular_function	nuclease activity
D	0004519	molecular_function	endonuclease activity
D	0006281	biological_process	DNA repair

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
B	PRO89-LYS98

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

Chain	Residue	Details
B	ASP251-TRP267

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

Chain	Residue	Details
B	ASN277-SER288

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: ACT_SITE => ECO:0000269|PubMed:15380100

Chain	Residue	Details
D	TYR171
B	TYR171

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site_id	SWS_FT_FI2
Number of Residues	2
Details	ACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX

Chain	Residue	Details
D	ASP210
B	ASP210

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site_id	SWS_FT_FI3
Number of Residues	2
Details	ACT_SITE: Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764

Chain	Residue	Details
B	HIS309
D	HIS309

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site_id	SWS_FT_FI4
Number of Residues	12
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00764

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

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	SITE: Transition state stabilizer => ECO:0000269|PubMed:8932375

Chain	Residue	Details
D	ASN212
B	ASN212

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site_id	SWS_FT_FI6
Number of Residues	2
Details	SITE: Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799

Chain	Residue	Details
D	ASP283
B	ASP283

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site_id	SWS_FT_FI7
Number of Residues	2
Details	SITE: Interaction with DNA substrate

Chain	Residue	Details
D	HIS309
B	HIS309

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site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
D	SER54
B	SER54

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site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694

Chain	Residue	Details
D	CYS65
D	CYS93
B	CYS65
B	CYS93

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site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
D	LYS197
B	LYS197

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site_id	SWS_FT_FI11
Number of Residues	2
Details	MOD_RES: Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352

Chain	Residue	Details
D	THR233
B	THR233

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site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:17403694

Chain	Residue	Details
B	CYS310
D	CYS310

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Catalytic Information from CSA

site_id	MCSA1
Number of Residues	8
Details	M-CSA 510

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

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site_id	MCSA2
Number of Residues	8
Details	M-CSA 510

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

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