Base excision repair (Homo sapiens)

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Description

Base excision repair is a cellular mechanism that repairs damaged DNA throughout the cell cycle. It is primarily responsible for removing small, non-helix-distorting base lesions from the genome.

Base excision repair is important for removing damaged bases that could otherwise cause mutations by mispairing, or could lead to breaks in DNA during replication.

BER is initiated by DNA glycosylases, which recognize and remove specific damaged or inappropriate bases, forming AP sites. These are then cleaved by an AP endonuclease. The resulting single-strand break can then be processed by either short-patch (where a single nucleotide is replaced) or long-patch BER (where 2-10 new nucleotides are synthesized). The choice between short- and long-patch repair is currently under investigation. Various factors are thought to influence this decision, including the type of lesion, the cell cycle stage, and whether the cell is terminally differentiated or actively dividing. Some lesions, such as oxidized or reduced AP sites, are resistant to pol β lyase activity and therefore must be processed by long-patch BER.

This pathway is based on information from REPAIRtoire (http://repairtoire.genesilico.pl/Pathway/4/), Wikipedia (https://en.wikipedia.org/wiki/Base_excision_repair) and KEGG (https://www.genome.jp/dbget-bin/www_bget?map03410). The description was adapted from REPAIRtoire, layout is based on KEGG.

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Quality Tags

Ontology Terms

 

Bibliography

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  1. ''KEGG''; https://www.genome.jp/dbget-bin/www_bget?map03410,
  2. ''REPAIRtoire Base excision repair''; REPAIRtoire,
  3. Krwawicz J, Arczewska KD, Speina E, Maciejewska A, Grzesiuk E; ''Bacterial DNA repair genes and their eukaryotic homologues: 1. Mutations in genes involved in base excision repair (BER) and DNA-end processors and their implication in mutagenesis and human disease.''; Acta Biochim Pol, 2007 PubMed Europe PMC Scholia
  4. Almeida KH, Sobol RW; ''A unified view of base excision repair: lesion-dependent protein complexes regulated by post-translational modification.''; DNA Repair (Amst), 2007 PubMed Europe PMC Scholia
  5. Moen MN, Knævelsrud I, Haugland GT, Grøsvik K, Birkeland NK, Klungland A, Bjelland S; ''Uracil-DNA glycosylase of Thermoplasma acidophilum directs long-patch base excision repair, which is promoted by deoxynucleoside triphosphates and ATP/ADP, into short-patch repair.''; J Bacteriol, 2011 PubMed Europe PMC Scholia
  6. Ikeda S, Seki S; ''[Base excision repair: DNA glycosylase and AP endonuclease].''; Tanpakushitsu Kakusan Koso, 2001 PubMed Europe PMC Scholia

History

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CompareRevisionActionTimeUserComment
142462view01:19, 21 February 2026Khanspersfixed curation issues
140982view11:29, 31 October 2025EweitzClear deprecated metadata rendering
136387view01:39, 1 February 2025Khanspersupdated reference
136386view01:38, 1 February 2025KhanspersModified description
136369view19:30, 31 January 2025KhanspersModified description
136368view19:28, 31 January 2025Khanspersupdated reference
127650view23:16, 13 November 2023Khanspersadded id and db for repairtoire lit ref
125305view17:47, 31 January 2023LarsgwFix reference
119239view19:09, 22 June 2021Finterlyadded KEGG biopax information
117660view11:52, 22 May 2021EweitzModified title
110588view21:08, 19 May 2020Khanspersminor update
108597view23:49, 9 January 2020KhanspersModified description
108050view00:41, 27 November 2019Khanspersadded references
108049view00:39, 27 November 2019KhanspersModified description
108032view22:37, 23 November 2019KhanspersOntology Term : 'DNA repair pathway' added !
108031view22:37, 23 November 2019KhanspersOntology Term : 'base excision repair pathway' added !
108030view22:36, 23 November 2019KhanspersModified description
108029view22:26, 23 November 2019Khanspersfixed interaction
108028view22:25, 23 November 2019Khanspersupdated complexes
108027view22:24, 23 November 2019KhanspersAdded PARPs
108026view01:16, 23 November 2019KhanspersNew pathway

External references

DataNodes

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NameTypeDatabase referenceComment
ADPRSGeneProductADPRS (HGNC)
APEX1GeneProductENSG00000100823 (Ensembl)
APTXGeneProductAPTX (HGNC)
FEN1GeneProductENSG00000168496 (Ensembl)
HMGB1GeneProductENSG00000189403 (Ensembl)
LIG1GeneProductENSG00000105486 (Ensembl)
LIG1GeneProductLIG1 (HGNC)
LIG3GeneProductENSG00000005156 (Ensembl)
MBD4GeneProductENSG00000129071 (Ensembl)
MPGGeneProductENSG00000103152 (Ensembl)
MUTYHGeneProductENSG00000132781 (Ensembl)
NEIL1GeneProduct79661 (Entrez Gene)
NEIL2GeneProductENSG00000154328 (Ensembl)
NEIL3GeneProductENSG00000109674 (Ensembl)
NTHL1GeneProductENSG00000065057 (Ensembl)
OGG1GeneProductENSG00000114026 (Ensembl)
PARP1GeneProductENSG00000143799 (Ensembl)
PARP2GeneProductENSG00000129484 (Ensembl)
PARP3GeneProductPARP3 (HGNC)
PARP4GeneProductPARP4 (HGNC)
PARPGGeneProductPARPG (HGNC)
PCNAGeneProductENSG00000132646 (Ensembl)
PNKPGeneProductENSG00000039650 (Ensembl) PKNP has a kinase domain which phosphorylates 5' hydroxyl ends, and a phosphatase domain, which removes phosphates from 3' ends.
POLBGeneProductENSG00000070501 (Ensembl)
POLD1GeneProductENSG00000062822 (Ensembl)
POLD2GeneProductENSG00000106628 (Ensembl)
POLD3GeneProductENSG00000077514 (Ensembl)
POLD4GeneProductENSG00000175482 (Ensembl)
POLE2GeneProductENSG00000100479 (Ensembl)
POLE3GeneProductENSG00000148229 (Ensembl)
POLE4GeneProductENSG00000115350 (Ensembl)
POLEGeneProductENSG00000177084 (Ensembl)
POLG2GeneProductPOLG2 (HGNC)
POLGGeneProductPOLG (HGNC)
POLLGeneProductENSG00000166169 (Ensembl)
RFC1GeneProductRFC1 (HGNC)
RFC2GeneProductRFC2 (HGNC)
RFC3GeneProductRFC3 (HGNC)
RFC4GeneProductRFC4 (HGNC)
RFC5GeneProductRFC5 (HGNC)
SMUG1GeneProductENSG00000123415 (Ensembl)
TDGGeneProductENSG00000139372 (Ensembl)
TDP1GeneProduct55775 (Entrez Gene)
UNGGeneProductENSG00000076248 (Ensembl)
XRCC1GeneProductENSG00000073050 (Ensembl)

Annotated Interactions

No annotated interactions

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