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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA
 
Authors :  C. D. Mol, T. Izumi, S. Mitra, J. A. Tainer
Date :  15 Nov 99  (Deposition) - 02 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,U,V,X,Y
Biol. Unit 1:  B,X,Y  (1x)
Biol. Unit 2:  A,U,V  (1x)
Keywords :  Enzyme:Dna Complex, Dna Repair, Abasic Site, Lyase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. D. Mol, T. Izumi, S. Mitra, J. A. Tainer
Dna-Bound Structures And Mutants Reveal Abasic Dna Binding By Ape1 And Dna Repair Coordination
Nature V. 403 451 2000
PubMed-ID: 10667800  |  Reference-DOI: 10.1038/35000249
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*GP*TP*CP*CP*(3DR) P*CP*GP*AP*CP*GP*AP*CP*G)-3'
    ChainsX, U
    EngineeredYES
    Other DetailsDNA CONTAINS ABASIC NUCLEOTIDE 3DR
    SyntheticYES
 
Molecule 2 - 5'-D(*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)- 3'
    ChainsY, V
    EngineeredYES
    SyntheticYES
 
Molecule 3 - MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
    ChainsA, B
    EC Number4.2.99.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentAPE1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPE1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABUVXY
Biological Unit 1 (1x) B  XY
Biological Unit 2 (1x)A UV  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
13DR2Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:136 , GLN B:137BINDING SITE FOR RESIDUE SO4 B 2055

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DEW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:247 -Pro A:248
2Val B:247 -Pro B:248

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013455Q51HAPEX1_HUMANPolymorphism1048945A/BH51H
2UniProtVAR_014823I64VAPEX1_HUMANPolymorphism2307486A/BI64V
3UniProtVAR_019790D148EAPEX1_HUMANPolymorphism1130409A/BD148E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013455Q51HAPEX1_HUMANPolymorphism1048945BH51H
2UniProtVAR_014823I64VAPEX1_HUMANPolymorphism2307486BI64V
3UniProtVAR_019790D148EAPEX1_HUMANPolymorphism1130409BD148E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013455Q51HAPEX1_HUMANPolymorphism1048945AH51H
2UniProtVAR_014823I64VAPEX1_HUMANPolymorphism2307486AI64V
3UniProtVAR_019790D148EAPEX1_HUMANPolymorphism1130409AD148E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 8)

Asymmetric Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AP_NUCLEASE_F1_4PS51435 AP endonucleases family 1 profile.APEX1_HUMAN62-318
 
  2A:62-318
B:62-318
2AP_NUCLEASE_F1_1PS00726 AP endonucleases family 1 signature 1.APEX1_HUMAN89-98
 
  2A:89-98
B:89-98
3AP_NUCLEASE_F1_2PS00727 AP endonucleases family 1 signature 2.APEX1_HUMAN251-267
 
  2A:251-267
B:251-267
4AP_NUCLEASE_F1_3PS00728 AP endonucleases family 1 signature 3.APEX1_HUMAN277-288
 
  2A:277-288
B:277-288
Biological Unit 1 (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AP_NUCLEASE_F1_4PS51435 AP endonucleases family 1 profile.APEX1_HUMAN62-318
 
  1-
B:62-318
2AP_NUCLEASE_F1_1PS00726 AP endonucleases family 1 signature 1.APEX1_HUMAN89-98
 
  1-
B:89-98
3AP_NUCLEASE_F1_2PS00727 AP endonucleases family 1 signature 2.APEX1_HUMAN251-267
 
  1-
B:251-267
4AP_NUCLEASE_F1_3PS00728 AP endonucleases family 1 signature 3.APEX1_HUMAN277-288
 
  1-
B:277-288
Biological Unit 2 (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AP_NUCLEASE_F1_4PS51435 AP endonucleases family 1 profile.APEX1_HUMAN62-318
 
  1A:62-318
-
2AP_NUCLEASE_F1_1PS00726 AP endonucleases family 1 signature 1.APEX1_HUMAN89-98
 
  1A:89-98
-
3AP_NUCLEASE_F1_2PS00727 AP endonucleases family 1 signature 2.APEX1_HUMAN251-267
 
  1A:251-267
-
4AP_NUCLEASE_F1_3PS00728 AP endonucleases family 1 signature 3.APEX1_HUMAN277-288
 
  1A:277-288
-

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003980301cENSE00001531237chr14:20923400-2092349798APEX1_HUMAN-00--
1.2ENST000003980302ENSE00000889014chr14:20923737-20923862126APEX1_HUMAN1-20200--
1.3aENST000003980303aENSE00000652723chr14:20924073-20924260188APEX1_HUMAN20-82632A:41-82
B:40-82
42
43
1.4ENST000003980304ENSE00000652726chr14:20924827-20925019193APEX1_HUMAN83-147652A:83-147
B:83-147
65
65
1.5aENST000003980305aENSE00001842242chr14:20925150-20925895746APEX1_HUMAN147-3181722A:147-318
B:147-318
172
172

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:278
 aligned with APEX1_HUMAN | P27695 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:278
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
          APEX1_HUMAN    41 GPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
               SCOP domains d1dewa_ A: DNA repair endonuclease Hap1                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1dewA00 A:41-318  [code=3.60.10.10, no name defined]                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhheeeee..........eeeee.....eeee...hhhhh....eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh.hhhhhh.....hhhhhhhhhhhhhhh..eehhhhhh...........hhhhh.........eeeee.hhhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------H------------V-----------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------AP_NUCLEASE_F1_4  PDB: A:62-318 UniProt: 62-318                                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) ------------------------------------------------AP_NUCLEAS--------------------------------------------------------------------------------------------------------------------------------------------------------AP_NUCLEASE_F1_2 ---------AP_NUCLEASE_------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.3a  PDB: A:41-82 UniProt: 20-82    Exon 1.4  PDB: A:83-147 UniProt: 83-147                          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------Exon 1.5a  PDB: A:147-318 UniProt: 147-318                                                                                                                                   Transcript 1 (2)
                 1dew A  41 GPALYEDPPDHKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        

Chain B from PDB  Type:PROTEIN  Length:279
 aligned with APEX1_HUMAN | P27695 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:279
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309         
          APEX1_HUMAN    40 EGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
               SCOP domains d1dewb_ B: DNA repair endonuclease Hap1                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1dewB00 B:40-318  [code=3.60.10.10, no name defined]                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee.........hhhhhh.....eeeee..........eeeee.....eeee............eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhh............hhhhhhhhhhhhhhh..eehhhhhh..............hhhhhh.....eeeee.hhhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) -----------H------------V-----------------------------------------------------------------------------------E-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------AP_NUCLEASE_F1_4  PDB: B:62-318 UniProt: 62-318                                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) -------------------------------------------------AP_NUCLEAS--------------------------------------------------------------------------------------------------------------------------------------------------------AP_NUCLEASE_F1_2 ---------AP_NUCLEASE_------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.3a  PDB: B:40-82 UniProt: 20-82     Exon 1.4  PDB: B:83-147 UniProt: 83-147                          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------Exon 1.5a  PDB: B:147-318 UniProt: 147-318                                                                                                                                   Transcript 1 (2)
                 1dew B  40 EGPALYEDPPDHKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309         

Chain U from PDB  Type:DNA  Length:15
                                               
                 1dew U  31 GCGTCCxCGACGACG  45
                                  | 40     
                                 37-3DR    

Chain V from PDB  Type:DNA  Length:14
                                              
                 1dew V  47 GTCGTCGGGGACGC  60
                                    56    

Chain X from PDB  Type:DNA  Length:15
                                               
                 1dew X   1 GCGTCCxCGACGACG  15
                                  | 10     
                                  7-3DR    

Chain Y from PDB  Type:DNA  Length:14
                                              
                 1dew Y  17 GTCGTCGGGGACGC  30
                                    26    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DEW)

(-) Gene Ontology  (64, 64)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (APEX1_HUMAN | P27695)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003906    DNA-(apurinic or apyrimidinic site) endonuclease activity    Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER).
    GO:0051059    NF-kappaB binding    Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0031490    chromatin DNA binding    Interacting selectively and non-covalently with DNA that is assembled into chromatin.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0008311    double-stranded DNA 3'-5' exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule.
    GO:0008309    double-stranded DNA exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a double-stranded DNA molecule.
    GO:0003691    double-stranded telomeric DNA binding    Interacting selectively and non-covalently with double-stranded telomere-associated DNA.
    GO:0004520    endodeoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004528    phosphodiesterase I activity    Catalysis of the sequential hydrolytic removal of 5'-nucleotides from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016890    site-specific endodeoxyribonuclease activity, specific for altered base    Catalysis of the hydrolysis of ester linkages at specific sites within a deoxyribonucleic acid molecule by creating internal breaks.
    GO:0003713    transcription coactivator activity    A protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to activate the transcription of specific genes. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. Another type of coregulator activity is the bridging of a DNA-binding transcription factor to the basal transcription machinery. The Mediator complex, which bridges transcription factors and RNA polymerase, is also a transcription coactivator.
    GO:0003714    transcription corepressor activity    A protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to repress the transcription of specific genes. Corepressors often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. A third class occludes DNA-binding transcription factor protein-protein interaction domains. A third class of corepressors prevents interactions of DNA bound DNA-binding transcription factor with coactivators.
    GO:0004844    uracil DNA N-glycosylase activity    Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.
biological process
    GO:0080111    DNA demethylation    The removal of a methyl group from one or more nucleotides within an DNA molecule.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006286    base-excision repair, base-free sugar-phosphate removal    Excision of the sugar phosphate residue at an AP site, i.e. a deoxyribose sugar with a missing base, by a phosphodiesterase enzyme.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071320    cellular response to cAMP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0071417    cellular response to organonitrogen compound    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    GO:0071375    cellular response to peptide hormone stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0014912    negative regulation of smooth muscle cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell migration.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0045739    positive regulation of DNA repair    Any process that activates or increases the frequency, rate or extent of DNA repair.
    GO:1900087    positive regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that promotes the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0010243    response to organonitrogen compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        APEX1_HUMAN | P276951bix 1cqg 1cqh 1de8 1de9 1e9n 1hd7 2isi 2o3h 3u8u 4iem 4lnd 4qh9 4qhd 4qhe 5cfg 5dff 5dfh 5dfi 5dfj 5dg0

(-) Related Entries Specified in the PDB File

1bix CRYSTAL STRUCTURE OF UNCOMPLEXED APE1
1de8 CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ANOTHER ABASIC DNA
1de9 CRYSTAL STRUCTURE OF TERNARY APE1:DNA:MN2+ COMPLEX