1HD7
A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism
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 | 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 | 0016890 | molecular_function | site-specific endodeoxyribonuclease activity, specific for altered base |
A | 0031490 | molecular_function | chromatin DNA binding |
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 |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE PB A1319 |
Chain | Residue |
A | ASP70 |
A | GLU96 |
A | HOH2069 |
A | HOH2079 |
A | HOH2282 |
A | HOH2283 |
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 | 1 |
Details | ACT_SITE: ACT_SITE => ECO:0000269|PubMed:15380100 |
Chain | Residue | Details |
A | VAL172 |
site_id | SWS_FT_FI2 |
Number of Residues | 1 |
Details | ACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX |
Chain | Residue | Details |
A | LEU211 |
site_id | SWS_FT_FI3 |
Number of Residues | 1 |
Details | ACT_SITE: Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764 |
Chain | Residue | Details |
A | CYS310 |
site_id | SWS_FT_FI4 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00764 |
Chain | Residue | Details |
A | VAL69 | |
A | THR97 | |
A | LEU211 | |
A | VAL213 | |
A | HIS309 | |
A | CYS310 |
site_id | SWS_FT_FI5 |
Number of Residues | 1 |
Details | SITE: Cleavage; by granzyme A |
Chain | Residue | Details |
A | LYS32 |
site_id | SWS_FT_FI6 |
Number of Residues | 1 |
Details | SITE: Transition state stabilizer => ECO:0000269|PubMed:8932375 |
Chain | Residue | Details |
A | VAL213 |
site_id | SWS_FT_FI7 |
Number of Residues | 1 |
Details | SITE: Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799 |
Chain | Residue | Details |
A | TYR284 |
site_id | SWS_FT_FI8 |
Number of Residues | 1 |
Details | SITE: Interaction with DNA substrate |
Chain | Residue | Details |
A | CYS310 |
site_id | SWS_FT_FI9 |
Number of Residues | 2 |
Details | MOD_RES: N6-acetyllysine; by EP300 => ECO:0000269|PubMed:14633989 |
Chain | Residue | Details |
A | LYS7 | |
A | GLY8 |
site_id | SWS_FT_FI10 |
Number of Residues | 4 |
Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:20699270 |
Chain | Residue | Details |
A | THR28 | |
A | LYS32 | |
A | ASN33 | |
A | GLU36 |
site_id | SWS_FT_FI11 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
A | PRO55 |
site_id | SWS_FT_FI12 |
Number of Residues | 2 |
Details | MOD_RES: S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694 |
Chain | Residue | Details |
A | SER66 | |
A | LEU94 |
site_id | SWS_FT_FI13 |
Number of Residues | 1 |
Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
A | GLY198 |
site_id | SWS_FT_FI14 |
Number of Residues | 1 |
Details | MOD_RES: Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352 |
Chain | Residue | Details |
A | PRO234 |
site_id | SWS_FT_FI15 |
Number of Residues | 1 |
Details | MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:17403694 |
Chain | Residue | Details |
A | PRO311 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 5 |
Details | Annotated By Reference To The Literature 1ako |
Chain | Residue | Details |
A | ASN212 | |
A | HIS309 | |
A | ASN68 | |
A | ASP283 | |
A | ASP210 |
site_id | MCSA1 |
Number of Residues | 8 |
Details | M-CSA 510 |
Chain | Residue | Details |
A | GLY71 | metal ligand |
A | THR97 | metal ligand |
A | VAL172 | electrostatic stabiliser, metal ligand |
A | LEU211 | increase nucleophilicity, metal ligand, proton acceptor |
A | VAL213 | |
A | TYR284 | electrostatic stabiliser |
A | HIS309 | metal ligand |
A | CYS310 | electrostatic stabiliser, metal ligand |