Note that this term is does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. Class II AP endonuclease is a nuclease, but not Class I, III and IV.
GO:0003906
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DNA-(apurinic or apyrimidinic site) endonuclease activity
Molecular Function
Definition (GO:0003906 GONUTS page)
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).
Comments
Note that this term is does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. Class II AP endonuclease is a nuclease, but not Class I, III and IV.
Synonyms
Synonyms are alternative words or phrases closely related in meaning to the term name, with indication of the relationship between the name and synonym given by the synonym scope.
Synonym | Type |
---|---|
apurinic deoxyendoribonuclease activity | exact |
UV endonuclease | broad |
apyrimidinic deoxyendoribonuclease activity | exact |
apurinic/apyrimidinic endodeoxyribonuclease activity | exact |
endonuclease VIII activity | related |
abasic deoxyendoribonuclease activity | exact |
deoxyribonuclease (apurinic or apyrimidinic) activity | exact |
AP deoxyendoribonuclease activity | exact |
Ancestor Chart
Child Terms
This table lists all terms that are direct descendants (child terms) of GO:0003906
Child Term | Relationship to GO:0003906 |
---|---|
class I DNA-(apurinic or apyrimidinic site) endonuclease activity
|
is_a |
class II DNA-(apurinic or apyrimidinic site) endonuclease activity
|
is_a |
Annotation Guidance
Usage of this term is subject to the following annotation guidelines:
Annotating to catalytic activities using the IPI evidence code | Link |
Describing enzyme functions that catalyse multi-stage reactions | Link |
Annotation Blacklist
This list aims to correct incorrect annotations to UniProtKB accessions inferred from electronic annotation (IEA) methods that are supplied by the UniProt-GOA project to the GO Consortium:
Category | Entity Type | Entity ID | Taxon ID | Entity Name | Ancestor GO ID | Reason | Rule/Method ID |
---|---|---|---|---|---|---|---|
NOT-qualified manual | protein | P02521 | 9031 | ARLY1_CHICK | GO:0003824 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000304 from this reference: PMID:11258884 | |
NOT-qualified manual | protein | Q5NVR0 | 9601 | HMCES_PONAB | GO:0003906 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000250 from this reference: GO_REF:0000024 | |
NOT-qualified manual | protein | Q5XIJ1 | 10116 | HMCES_RAT | GO:0003906 | 2 NOT-qualified manual annotations exist with these evidence codes: ECO:0000250, ECO:0000266 from these references: GO_REF:0000024, GO_REF:0000096 | |
NOT-qualified manual | protein | Q5ZJT1 | 9031 | HMCES_CHICK | GO:0003906 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000250 from this reference: GO_REF:0000024 | |
NOT-qualified manual | protein | Q6IND6 | 8355 | HMCES_XENLA | GO:0003906 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000250 from this reference: GO_REF:0000024 | |
NOT-qualified manual | protein | Q6P7N4 | 8364 | HMCES_XENTR | GO:0003906 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000250 from this reference: GO_REF:0000024 | |
NOT-qualified manual | protein | Q7KGG1 | 7227 | Q7KGG1_DROME | GO:0003824 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000320 from this reference: PMID:11904370 | |
NOT-qualified manual | protein | Q7SIE0 | 9103 | ARLY1_MELGA | GO:0003824 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000304 from this reference: PMID:11258884 | |
NOT-qualified manual | protein | Q8MZ84 | 7227 | Q8MZ84_DROME | GO:0003824 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000320 from this reference: PMID:11904370 | |
NOT-qualified manual | protein | Q8R1M0 | 10090 | HMCES_MOUSE | GO:0003906 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000250 from this reference: GO_REF:0000024 |
Cross-references
Database | ID | Description |
---|---|---|
InterPro | IPR000214 | Zinc finger, DNA glycosylase/AP lyase-type |
InterPro | IPR005759 | Endonuclease III |
InterPro | IPR012092 | 8-oxoguanine DNA glycosylase/AP lyase Ogg |
InterPro | IPR012319 | Formamidopyrimidine-DNA glycosylase, catalytic domain |
InterPro | IPR015254 | N-glycosylase/DNA lyase-like |
InterPro | IPR015886 | DNA glycosylase/AP lyase, H2TH DNA-binding |
InterPro | IPR015887 | DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site |
InterPro | IPR016544 | N-glycosylase/DNA lyase |
InterPro | IPR020629 | Formamidopyrimidine-DNA glycosylase |
InterPro | IPR030841 | Endonuclease III-like protein 1 |
Replaces
This term can be used instead of these obsolete terms:
GO Identifier | GO Term Name | Reason |
---|---|---|
GO:0006286 | obsolete base-excision repair, base-free sugar-phosphate removal | consider GO:0003906 |
GO:0008845 | obsolete endonuclease VIII activity | consider GO:0003906 |
Co-occurring Terms
These tables show the number of times the term listed in the table has been co-annotated.
No co-occurrence statistics for GO:0003906 based on ALL annotations
The top 100 of 885 co-occurring terms
Co-occurring Term | PR | S% | #Together | #Compared |
---|---|---|---|---|
DNA-(apurinic or apyrimidinic site) endonuclease activity
|
1,189.86 | 100.00 | 163,834 | 163,834 |
class I DNA-(apurinic or apyrimidinic site) endonuclease activity
|
1,118.22 | 43.18 | 72,758 | 77,419 |
base-excision repair
|
511.35 | 42.62 | 160,672 | 373,869 |
DNA N-glycosylase activity
|
686.05 | 32.43 | 69,727 | 120,931 |
base-excision repair, AP site formation
|
527.14 | 20.52 | 45,318 | 102,291 |
8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
|
544.73 | 18.33 | 38,370 | 83,811 |
oxidized purine nucleobase lesion DNA N-glycosylase activity
|
918.45 | 17.42 | 30,081 | 38,970 |
double-stranded DNA 3'-5' DNA exonuclease activity
|
536.62 | 14.59 | 29,055 | 64,424 |
phosphoric diester hydrolase activity
|
234.17 | 14.06 | 54,084 | 274,809 |
oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
|
1,060.50 | 12.13 | 20,168 | 22,628 |
Totals | 1809077 | 98463665 |
No co-occurrence statistics for GO:0003906 based on MANUAL annotations
The top 100 of 324 co-occurring terms
Co-occurring Term | PR | S% | #Together | #Compared |
---|---|---|---|---|
DNA-(apurinic or apyrimidinic site) endonuclease activity
|
1,668.99 | 100.00 | 774 | 774 |
double-stranded DNA 3'-5' DNA exonuclease activity
|
1,630.38 | 48.53 | 380 | 389 |
base-excision repair
|
924.15 | 47.86 | 603 | 1,089 |
phosphoric diester hydrolase activity
|
673.75 | 30.82 | 438 | 1,085 |
oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
|
1,377.89 | 17.66 | 142 | 172 |
DNA N-glycosylase activity
|
1,097.29 | 14.23 | 119 | 181 |
base-excision repair, AP site formation
|
461.26 | 11.73 | 131 | 474 |
chloroplast nucleoid
|
309.96 | 5.19 | 52 | 280 |
nucleotide-excision repair
|
94.43 | 4.44 | 132 | 2,333 |
8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
|
171.81 | 2.75 | 28 | 272 |
Totals | 3627 | 35266 |
Change Log
- All changes
- All changes
- Term
- Term
- Definition / Synonyms
- Definition / Synonyms
- Relationships
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- Cross-references
- Cross-references
- Other
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Timestamp | Action | Category | Detail |
---|---|---|---|
2021-10-30 | Deleted | RELATION | is a GO:0004519 (endonuclease activity) |
2021-06-18 | Added | RELATION | is a GO:0004519 (endonuclease activity) |
2019-04-01 | Added | XREF | Reactome:R-HSA-5649711 |
2019-04-01 | Deleted | XREF | reactome:R-HSA-110375 |
2019-04-01 | Deleted | XREF | reactome:R-HSA-5649725 |
2019-04-01 | Added | XREF | Reactome:R-HSA-110375 |
2019-04-01 | Deleted | XREF | reactome:R-HSA-5649711 |
2019-04-01 | Added | XREF | Reactome:R-HSA-5649725 |
2018-12-11 | Added | XREF | reactome:R-HSA-110375 |
2018-12-11 | Added | XREF | reactome:R-HSA-5649711 |
Timestamp | Action | Category | Detail |
---|---|---|---|
2018-03-10 | Updated | TERM | DNA-(apurinic or apyrimidinic site) endonuclease activity |
2003-03-19 | Updated | TERM | DNA-(apurinic or apyrimidinic site) lyase activity |
2002-02-06 | Updated | TERM | DNA-(apurinic or apyrimidinic site) lyase |
2001-04-03 | Updated | TERM | DNA-(apurinic or apyrimidinic site) lyase |
2001-03-30 | Added | TERM | DNA-(apurinic or apyrimidinic site) lyase |
Timestamp | Action | Category | Detail |
---|---|---|---|
2018-03-10 | Deleted | SYNONYM | DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase activity |
2018-03-10 | Added | SYNONYM | apurinic/apyrimidinic endodeoxyribonuclease activity |
2018-03-10 | Added | SYNONYM | apyrimidinic deoxyendoribonuclease activity |
2018-03-10 | Added | SYNONYM | apurinic deoxyendoribonuclease activity |
2018-03-10 | Added | SYNONYM | abasic deoxyendoribonuclease activity |
2018-03-10 | Added | SYNONYM | AP deoxyendoribonuclease activity |
2018-03-10 | Deleted | SYNONYM | AP site-DNA 5'-phosphomonoester-lyase activity |
2018-03-10 | Deleted | SYNONYM | AP lyase activity |
2018-03-10 | Deleted | SYNONYM | endodeoxyribonuclease (apurinic or apyrimidinic) activity |
2017-07-28 | Added | SYNONYM | UV endonuclease |
2017-07-28 | Deleted | SYNONYM | E. coli endonuclease III |
2017-07-28 | Deleted | SYNONYM | Phage-T4 UV endonuclease activity |
2017-07-28 | Deleted | SYNONYM | X-ray endonuclease III |
2017-07-28 | Deleted | SYNONYM | E. coli endonuclease III activity |
2017-07-28 | Deleted | SYNONYM | Phage-T(4) UV endonuclease activity |
2017-07-28 | Deleted | SYNONYM | Micrococcus luteus UV endonuclease activity |
2017-07-28 | Deleted | SYNONYM | phage-T4 UV endonuclease |
2017-07-28 | Deleted | SYNONYM | micrococcus luteus UV endonuclease |
2017-07-28 | Deleted | SYNONYM | AP endonuclease class I activity |
2017-07-28 | Deleted | DEFINITION | Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. |
2017-07-28 | Added | DEFINITION | 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). |
2008-11-07 | Added | SYNONYM | E. coli endonuclease III activity |
2008-11-07 | Deleted | SYNONYM | E.coli endonuclease III activity |
2008-05-13 | Added | DEFINITION | Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. |
2008-05-12 | Deleted | DEFINITION | Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. |
2007-11-08 | Added | SYNONYM | phage-T4 UV endonuclease |
2007-11-08 | Added | SYNONYM | micrococcus luteus UV endonuclease |
2007-11-08 | Added | SYNONYM | X-ray endonuclease III |
2007-11-08 | Added | SYNONYM | E. coli endonuclease III |
2007-11-08 | Added | SYNONYM | DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase activity |
2007-11-08 | Added | SYNONYM | AP site-DNA 5'-phosphomonoester-lyase activity |
2007-09-06 | Added | SYNONYM | Phage-T(4) UV endonuclease activity |
2007-09-06 | Added | SYNONYM | Phage-T4 UV endonuclease activity |
2007-09-06 | Added | SYNONYM | endodeoxyribonuclease (apurinic or apyrimidinic) activity |
2007-09-06 | Added | SYNONYM | deoxyribonuclease (apurinic or apyrimidinic) activity |
2007-09-06 | Added | SYNONYM | Micrococcus luteus UV endonuclease activity |
2007-09-06 | Added | SYNONYM | E.coli endonuclease III activity |
2007-09-06 | Added | SYNONYM | AP lyase activity |
2007-09-06 | Added | SYNONYM | AP endonuclease class I activity |
2007-08-09 | Added | SYNONYM | endonuclease VIII activity |
2007-08-09 | Deleted | SYNONYM | endonuclease VIII activity |
2005-08-10 | Added | SYNONYM | endonuclease VIII activity |
2002-11-27 | Added | DEFINITION | Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. |
Timestamp | Action | Category | Detail |
---|---|---|---|
2021-10-30 | Deleted | RELATION | is a GO:0004519 (endonuclease activity) |
2021-06-18 | Added | RELATION | is a GO:0004519 (endonuclease activity) |
2018-03-10 | Deleted | RELATION | is a GO:0016835 (carbon-oxygen lyase activity) |
2017-09-19 | Added | RELATION | is a GO:0140097 (catalytic activity, acting on DNA) |
2017-07-28 | Deleted | RELATION | is a GO:0004520 (DNA endonuclease activity) |
2014-01-29 | Added | RELATION | is a GO:0004520 (DNA endonuclease activity) |
2008-04-01 | Updated | RELATION | is a GO:0016835 (carbon-oxygen lyase activity) |
Timestamp | Action | Category | Detail |
---|---|---|---|
2019-04-01 | Added | XREF | Reactome:R-HSA-5649711 |
2019-04-01 | Deleted | XREF | reactome:R-HSA-110375 |
2019-04-01 | Deleted | XREF | reactome:R-HSA-5649725 |
2019-04-01 | Added | XREF | Reactome:R-HSA-110375 |
2019-04-01 | Deleted | XREF | reactome:R-HSA-5649711 |
2019-04-01 | Added | XREF | Reactome:R-HSA-5649725 |
2018-12-11 | Added | XREF | reactome:R-HSA-110375 |
2018-12-11 | Added | XREF | reactome:R-HSA-5649711 |
2018-12-11 | Added | XREF | reactome:R-HSA-5649725 |
2018-03-10 | Deleted | XREF | EC:4.2.99.18 |
2018-03-10 | Deleted | XREF | MetaCyc:4.2.99.18-RXN |
2003-10-27 | Added | XREF | MetaCyc:4.2.99.18-RXN |
2001-03-30 | Added | XREF | EC:4.2.99.18 |
Timestamp | Action | Category | Detail |
---|
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