ENTRY       gmx03410                    Pathway
NAME        Base excision repair - Glycine max (soybean)
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 gmx03410  Base excision repair
DBLINKS     GO: 0006284 0006285 0006286 0006287 0006288
ORGANISM    Glycine max (soybean) [GN:gmx]
GENE        100806161  formamidopyrimidine-DNA glycosylase isoform X2 [KO:K10563] [EC:3.2.2.23 4.2.99.18]
            100789749  N-glycosylase/DNA lyase OGG1 [KO:K03660] [EC:3.2.2.- 4.2.99.18]
            100818398  endonuclease III homolog 1, chloroplastic [KO:K10773] [EC:4.2.99.18]
            100802952  putative DNA glycosylase At3g47830 [KO:K10773] [EC:4.2.99.18]
            100793690  putative DNA glycosylase At3g47830 [KO:K10773] [EC:4.2.99.18]
            100805799  endonuclease III homolog 2, chloroplastic isoform X1 [KO:K10773] [EC:4.2.99.18]
            100788160  DNA-3-methyladenine glycosylase 1-like [KO:K01247] [EC:3.2.2.21]
            100790760  probable DNA-3-methyladenine glycosylase 2 [KO:K01247] [EC:3.2.2.21]
            100306457  methyladenine glycosylase domain-containing protein [KO:K01246] [EC:3.2.2.20]
            100810677  DNA-3-methyladenine glycosylase [KO:K01246] [EC:3.2.2.20]
            100801026  probable GMP synthase [glutamine-hydrolyzing] [KO:K01246] [EC:3.2.2.20]
            100791725  probable GMP synthase [glutamine-hydrolyzing] [KO:K01246] [EC:3.2.2.20]
            100801163  DNA-3-methyladenine glycosylase 1 [KO:K01246] [EC:3.2.2.20]
            100793449  uncharacterized protein LOC100793449 [KO:K01246] [EC:3.2.2.20]
            100793991  uncharacterized protein LOC100793991 [KO:K01246] [EC:3.2.2.20]
            100813637  DNA-3-methyladenine glycosylase I-like [KO:K01246] [EC:3.2.2.20]
            100817116  DNA-3-methyladenine glycosylase 1 [KO:K01246] [EC:3.2.2.20]
            100783263  probable GMP synthase [glutamine-hydrolyzing] [KO:K01246] [EC:3.2.2.20]
            100785912  probable GMP synthase [glutamine-hydrolyzing] [KO:K01246] [EC:3.2.2.20]
            100805836  probable GMP synthase [glutamine-hydrolyzing] [KO:K01246] [EC:3.2.2.20]
            100814780  uncharacterized protein LOC100814780 [KO:K01246] [EC:3.2.2.20]
            100811352  probable GMP synthase [glutamine-hydrolyzing] isoform X1 [KO:K01246] [EC:3.2.2.20]
            100818241  uracil-DNA glycosylase, mitochondrial isoform X2 [KO:K03648] [EC:3.2.2.27]
            100818039  LOW QUALITY PROTEIN: uracil-DNA glycosylase, mitochondrial [KO:K03648] [EC:3.2.2.27]
            102664624  uracil-DNA glycosylase, mitochondrial [KO:K03648] [EC:3.2.2.27]
            100818278  adenine DNA glycosylase isoform X1 [KO:K03575] [EC:3.2.2.31]
            102669741  adenine DNA glycosylase [KO:K03575] [EC:3.2.2.31]
            100813424  DNA-3-methyladenine glycosylase isoform X1 [KO:K03652] [EC:3.2.2.21]
            100776653  DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic isoform X2 [KO:K01142] [EC:3.1.11.2]
            100781120  DNA-(apurinic or apyrimidinic site) endonuclease 2 [KO:K10772] [EC:4.2.99.18]
            100797016  DNA polymerase I A, chloroplastic/mitochondrial [KO:K02335] [EC:2.7.7.7]
            100807239  DNA polymerase I A, chloroplastic/mitochondrial [KO:K02335] [EC:2.7.7.7]
            100790704  DNA polymerase I B, chloroplastic/mitochondrial isoform X1 [KO:K02335] [EC:2.7.7.7]
            100820492  DNA polymerase lambda [KO:K03512] [EC:2.7.7.7 4.2.99.-]
            100818448  uncharacterized protein LOC100818448 [KO:K10803]
            100780160  DNA-repair protein XRCC1 [KO:K10803]
            548079  proliferating cell nuclear antigen [KO:K04802]
            100817651  proliferating cell nuclear antigen [KO:K04802]
            100780038  proliferating cell nuclear antigen [KO:K04802]
            548092  POLD1; DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
            100817379  DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
            100780072  DNA polymerase delta small subunit [KO:K02328]
            100805951  DNA polymerase delta small subunit isoform X1 [KO:K02328]
            100812372  DNA polymerase delta subunit 3 [KO:K03504]
            100793247  uncharacterized protein LOC100793247 isoform X1 [KO:K03504]
            100778329  DNA polymerase delta subunit 4 [KO:K03505]
            100799459  DNA polymerase delta subunit 4 [KO:K03505]
            100812003  DNA polymerase epsilon catalytic subunit A [KO:K02324] [EC:2.7.7.7]
            100778115  LOW QUALITY PROTEIN: DNA polymerase epsilon catalytic subunit A-like [KO:K02324] [EC:2.7.7.7]
            100784116  DNA polymerase epsilon subunit B isoform X2 [KO:K02325] [EC:2.7.7.7]
            100819488  DNA polymerase epsilon subunit 3 [KO:K02326] [EC:2.7.7.7]
            100306382  uncharacterized protein LOC100306382 [KO:K02326] [EC:2.7.7.7]
            100783155  DNA ligase 1 [KO:K10747] [EC:6.5.1.1 6.5.1.6 6.5.1.7]
            100815900  poly [ADP-ribose] polymerase 1 [KO:K24070] [EC:2.4.2.30]
            100800968  poly [ADP-ribose] polymerase 1 isoform X1 [KO:K24070] [EC:2.4.2.30]
            548024  PARP3; protein ADP-ribosyltransferase PARP3 [KO:K10798] [EC:2.4.2.30]
            100788978  protein ADP-ribosyltransferase PARP3 isoform X2 [KO:K10798] [EC:2.4.2.30]
            100814110  poly [ADP-ribose] polymerase 2-A [KO:K10798] [EC:2.4.2.30]
            100808044  flap endonuclease 1 [KO:K04799] [EC:3.1.-.-]
            100792878  flap endonuclease 1-like [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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