1BIX
THE CRYSTAL STRUCTURE OF THE HUMAN DNA REPAIR ENDONUCLEASE HAP1 SUGGESTS THE RECOGNITION OF EXTRA-HELICAL DEOXYRIBOSE AT DNA ABASIC SITES
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 | 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 | 5 |
| Details | BINDING SITE FOR RESIDUE SM A 400 |
| Chain | Residue |
| A | GLU216 |
| A | GLU217 |
| A | GLU242 |
| A | GLN245 |
| A | HOH566 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SM A 401 |
| Chain | Residue |
| A | ASP70 |
| A | GLU96 |
| A | HOH563 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SM A 402 |
| Chain | Residue |
| A | GLU46 |
| A | ASP148 |
| A | GLU150 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SM A 403 |
| Chain | Residue |
| A | ASP124 |
| A | GLU126 |
| A | LEU318 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PT A 404 |
| Chain | Residue |
| A | MET271 |
| A | LYS276 |
| site_id | ROX |
| Number of Residues | 1 |
| Details | CYS 65 HAS BEEN PROPOSED TO BE INVOLVED IN THE REDUCTIVE ACTIVATION OF A NUMBER OF TRANSCRIPTION FACTORS INCLUDING FOS/JUN AND P53. |
| Chain | Residue |
| A | CYS65 |
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 | 3 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:20699270 |
| Chain | Residue | Details |
| A | LYS32 | |
| A | ASN33 | |
| A | GLU36 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | PRO55 |
| site_id | SWS_FT_FI11 |
| 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_FI12 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | GLY198 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352 |
| Chain | Residue | Details |
| A | PRO234 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 1 |
| Details | MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:17403694 |
| Chain | Residue | Details |
| A | PRO311 |
Catalytic Information from CSA
| 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 |
