ENTRY       mtr03410                    Pathway
NAME        Base excision repair - Medicago truncatula (barrel medic)
DESCRIPTION Base excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair initiated by lesion-specific DNA glycosylases and completed by either of the two sub-pathways: short-patch BER where only one nucleotide is replaced and long-patch BER where 2-13 nucleotides are replaced. Each sub-pathway of BER relies on the formation of protein complexes that assemble at the site of the DNA lesion and facilitate repair in a coordinated fashion. This process of complex formation appears to provide an increase in specificity and efficiency to the BER pathway, thereby facilitating the maintenance of genome integrity by preventing the accumulation of highly toxic repair intermediates.
CLASS       Genetic Information Processing; Replication and repair
PATHWAY_MAP mtr03410  Base excision repair
DBLINKS     GO: 0006284 0006285 0006286 0006287 0006288
ORGANISM    Medicago truncatula (barrel medic) [GN:mtr]
GENE        11435290  formamidopyrimidine-DNA glycosylase isoform X1 [KO:K10563] [EC:3.2.2.23 4.2.99.18]
            11411506  N-glycosylase/DNA lyase OGG1 [KO:K03660] [EC:3.2.2.- 4.2.99.18]
            11434742  endonuclease III homolog 2, chloroplastic isoform X1 [KO:K10773] [EC:4.2.99.18]
            11405585  putative DNA glycosylase At3g47830 [KO:K10773] [EC:4.2.99.18]
            25492651  endonuclease III homolog 1, chloroplastic isoform X1 [KO:K10773] [EC:4.2.99.18]
            25490192  probable DNA-3-methyladenine glycosylase 2 [KO:K01247] [EC:3.2.2.21]
            11416684  probable DNA-3-methyladenine glycosylase 2 [KO:K01247] [EC:3.2.2.21]
            11425230  DNA-3-methyladenine glycosylase [KO:K01246] [EC:3.2.2.20]
            11445011  uncharacterized protein LOC11445011 [KO:K01246] [EC:3.2.2.20]
            25479532  DNA-3-methyladenine glycosylase 1 isoform X1 [KO:K01246] [EC:3.2.2.20]
            25502437  probable GMP synthase [glutamine-hydrolyzing] [KO:K01246] [EC:3.2.2.20]
            11433926  probable GMP synthase [glutamine-hydrolyzing] [KO:K01246] [EC:3.2.2.20]
            11439558  probable GMP synthase [glutamine-hydrolyzing] [KO:K01246] [EC:3.2.2.20]
            25490178  DNA-3-methyladenine glycosylase 1 [KO:K01246] [EC:3.2.2.20]
            25492828  uracil-DNA glycosylase, mitochondrial [KO:K03648] [EC:3.2.2.27]
            25492830  uracil-DNA glycosylase, mitochondrial [KO:K03648] [EC:3.2.2.27]
            25492833  uracil-DNA glycosylase, mitochondrial [KO:K03648] [EC:3.2.2.27]
            25500763  adenine DNA glycosylase isoform X1 [KO:K03575] [EC:3.2.2.31]
            11446465  DNA-3-methyladenine glycosylase [KO:K03652] [EC:3.2.2.21]
            25479885  methyl-CpG-binding domain protein 4-like protein [KO:K10801] [EC:3.2.2.-]
            25479887  methyl-CpG-binding domain protein 4-like protein [KO:K10801] [EC:3.2.2.-]
            25483315  DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic isoform X1 [KO:K01142] [EC:3.1.11.2]
            11443192  DNA-(apurinic or apyrimidinic site) endonuclease 2 [KO:K10772] [EC:4.2.99.18]
            11444798  DNA polymerase I A, chloroplastic/mitochondrial isoform X1 [KO:K02335] [EC:2.7.7.7]
            11436067  DNA polymerase I A, chloroplastic/mitochondrial [KO:K02335] [EC:2.7.7.7]
            11444264  DNA polymerase I A, chloroplastic/mitochondrial isoform X2 [KO:K02335] [EC:2.7.7.7]
            25498091  DNA polymerase lambda [KO:K03512] [EC:2.7.7.7 4.2.99.-]
            11418046  DNA polymerase lambda [KO:K03512] [EC:2.7.7.7 4.2.99.-]
            11442049  DNA-repair protein XRCC1 [KO:K10803]
            25490757  proliferating cell nuclear antigen [KO:K04802]
            25489857  DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
            11437014  DNA polymerase delta small subunit [KO:K02328]
            11408397  DNA polymerase delta subunit 3 isoform X1 [KO:K03504]
            25493347  DNA polymerase delta subunit 4 [KO:K03505]
            25493349  DNA polymerase delta subunit 4 [KO:K03505]
            25485289  DNA polymerase delta subunit 4 [KO:K03505]
            11445193  DNA polymerase epsilon catalytic subunit A isoform X1 [KO:K02324] [EC:2.7.7.7]
            25496685  DNA polymerase epsilon subunit B [KO:K02325] [EC:2.7.7.7]
            25492285  DNA polymerase epsilon subunit 3 [KO:K02326] [EC:2.7.7.7]
            25492370  DNA ligase 1 [KO:K10747] [EC:6.5.1.1 6.5.1.6 6.5.1.7]
            25499226  poly [ADP-ribose] polymerase 1 [KO:K24070] [EC:2.4.2.30]
            25484752  poly [ADP-ribose] polymerase 2 isoform X1 [KO:K10798] [EC:2.4.2.30]
            11444603  protein ADP-ribosyltransferase PARP3 [KO:K10798] [EC:2.4.2.30]
            11412823  flap endonuclease 1 [KO:K04799] [EC:3.1.-.-]
REFERENCE   PMID:17893748
  AUTHORS   Krwawicz J, Arczewska KD, Speina E, Maciejewska A, Grzesiuk E.
  TITLE     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.
  JOURNAL   Acta Biochim Pol 54:413-34 (2007)
REFERENCE   PMID:17337257
  AUTHORS   Almeida KH, Sobol RW.
  TITLE     A unified view of base excision repair: lesion-dependent protein complexes regulated by post-translational modification.
  JOURNAL   DNA Repair (Amst) 6:695-711 (2007)
            DOI:10.1016/j.dnarep.2007.01.009
REFERENCE   PMID:21665970
  AUTHORS   Moen MN, Knaevelsrud I, Haugland GT, Grosvik K, Birkeland NK, Klungland A, Bjelland S
  TITLE     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.
  JOURNAL   J Bacteriol 193:4495-508 (2011)
            DOI:10.1128/JB.00233-11
REFERENCE   PMID:11436317
  AUTHORS   Ikeda S, Seki S.
  TITLE     [Base excision repair: DNA glycosylase and AP endonuclease]
  JOURNAL   Tanpakushitsu Kakusan Koso 46:916-23 (2001)
KO_PATHWAY  ko03410
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