This term is obsolete.
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 JSON

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.

244,316 annotations

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
deoxyribonuclease (apurinic or apyrimidinic) activity exact
UV endonuclease broad
AP deoxyendoribonuclease activity exact
abasic deoxyendoribonuclease activity exact
apurinic deoxyendoribonuclease activity exact
apyrimidinic deoxyendoribonuclease activity exact
apurinic/apyrimidinic endodeoxyribonuclease activity exact
endonuclease VIII activity related

Ancestor Chart

Ancestor chart for GO:0003906
Chart options
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 877 co-occurring terms
Co-occurring Term PR S% #Together #Compared
DNA-(apurinic or apyrimidinic site) endonuclease activity
1,186.31 100.00 167,035 167,035
base-excision repair
509.39 42.58 163,792 381,448
class I DNA-(apurinic or apyrimidinic site) endonuclease activity
1,114.70 42.01 72,116 76,749
DNA N-glycosylase activity
594.45 30.31 72,493 144,669
base-excision repair, AP site formation
522.16 20.38 45,946 104,386
8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
543.47 18.32 39,080 85,306
oxidized purine nucleobase lesion DNA N-glycosylase activity
914.94 17.39 30,628 39,712
double-stranded DNA 3'-5' DNA exonuclease activity
536.27 14.64 29,719 65,743
phosphoric diester hydrolase activity
230.32 13.94 55,236 284,508
oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
1,057.80 12.25 20,776 23,300
Totals 1785339 102696525
No co-occurrence statistics for GO:0003906 based on MANUAL annotations
The top 100 of 317 co-occurring terms
Co-occurring Term PR S% #Together #Compared
DNA-(apurinic or apyrimidinic site) endonuclease activity
1,551.14 100.00 910 910
double-stranded DNA 3'-5' DNA exonuclease activity
1,523.27 53.54 492 501
base-excision repair
891.96 50.28 728 1,266
phosphoric diester hydrolase activity
694.29 34.65 551 1,231
oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
1,245.86 15.95 151 188
DNA N-glycosylase activity
983.65 13.20 130 205
base-excision repair, AP site formation
428.32 10.96 140 507
chloroplast nucleoid
291.80 4.93 57 303
nucleotide-excision repair
91.01 4.44 140 2,386
8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
149.25 2.39 28 291
Totals 4959 252415

Change Log

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-110375
2019-04-01 Added XREF Reactome:R-HSA-5649711
2019-04-01 Added XREF Reactome:R-HSA-5649725
2019-04-01 Deleted XREF reactome:R-HSA-5649711
2019-04-01 Deleted XREF reactome:R-HSA-5649725
2019-04-01 Deleted XREF reactome:R-HSA-110375
2018-12-11 Added XREF reactome:R-HSA-5649711
2018-12-11 Added XREF reactome:R-HSA-5649725
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 Added SYNONYM apurinic deoxyendoribonuclease activity
2018-03-10 Added SYNONYM AP deoxyendoribonuclease activity
2018-03-10 Added SYNONYM abasic deoxyendoribonuclease activity
2018-03-10 Added SYNONYM apyrimidinic deoxyendoribonuclease activity
2018-03-10 Added SYNONYM apurinic/apyrimidinic endodeoxyribonuclease activity
2018-03-10 Deleted SYNONYM DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase activity
2018-03-10 Deleted SYNONYM endodeoxyribonuclease (apurinic or apyrimidinic) activity
2018-03-10 Deleted SYNONYM AP lyase activity
2018-03-10 Deleted SYNONYM AP site-DNA 5'-phosphomonoester-lyase activity
2017-07-28 Deleted SYNONYM E. coli endonuclease III
2017-07-28 Added SYNONYM 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 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 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).
2017-07-28 Deleted SYNONYM Phage-T4 UV endonuclease activity
2017-07-28 Deleted SYNONYM X-ray endonuclease III
2008-11-07 Deleted SYNONYM E.coli endonuclease III activity
2008-11-07 Added 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 AP site-DNA 5'-phosphomonoester-lyase activity
2007-11-08 Added SYNONYM DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase activity
2007-11-08 Added SYNONYM E. coli endonuclease III
2007-11-08 Added SYNONYM X-ray endonuclease III
2007-11-08 Added SYNONYM micrococcus luteus UV endonuclease
2007-11-08 Added SYNONYM phage-T4 UV endonuclease
2007-09-06 Added SYNONYM deoxyribonuclease (apurinic or apyrimidinic) 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
2007-09-06 Added SYNONYM endodeoxyribonuclease (apurinic or apyrimidinic) activity
2007-09-06 Added SYNONYM Micrococcus luteus UV endonuclease activity
2007-09-06 Added SYNONYM Phage-T4 UV endonuclease activity
2007-09-06 Added SYNONYM Phage-T(4) UV endonuclease activity
2007-08-09 Deleted SYNONYM endonuclease VIII activity
2007-08-09 Added 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-110375
2019-04-01 Added XREF Reactome:R-HSA-5649711
2019-04-01 Added XREF Reactome:R-HSA-5649725
2019-04-01 Deleted XREF reactome:R-HSA-5649711
2019-04-01 Deleted XREF reactome:R-HSA-5649725
2019-04-01 Deleted XREF reactome:R-HSA-110375
2018-12-11 Added XREF reactome:R-HSA-5649711
2018-12-11 Added XREF reactome:R-HSA-5649725
2018-12-11 Added XREF reactome:R-HSA-110375
2018-03-10 Deleted XREF MetaCyc:4.2.99.18-RXN
2018-03-10 Deleted XREF EC:4.2.99.18
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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