KEGG   PATHWAY: dosa03410
Entry
dosa03410                   Pathway                                
Name
Base excision repair - Oryza sativa japonica (Japanese rice) (RAPDB)
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
dosa03410  Base excision repair
dosa03410

Other DBs
GO: 0006284 0006285 0006286 0006287 0006288
Organism
Oryza sativa japonica (Japanese rice) (RAPDB) [GN:dosa]
Gene
Os02t0552600-00  (RAP-DB) Os02g0552600; Similar to F8K7.14 protein. [KO:K03660] [EC:3.2.2.- 4.2.99.18]
Os06t0237900-00  (RAP-DB) Os06g0237900; Conserved hypothetical protein. [KO:K10773] [EC:3.2.2.- 4.2.99.18]
Os04t0673400-01  (RAP-DB) Os04g0673400; Similar to Uracil-DNA glycosylase. [KO:K03648] [EC:3.2.2.27]
Os12t0211400-00  (RAP-DB) Os12g0211400; A/G-specific adenine glycosylase MutY, bacterial form domain containing protein. [KO:K03575] [EC:3.2.2.31]
Os12t0212100-00  (RAP-DB) Os12g0212100; Similar to A/G-specific adenine DNA glycosylase. [KO:K03575] [EC:3.2.2.31]
Os02t0774500-01  (RAP-DB) Os02g0774500; Similar to DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase). [KO:K03652] [EC:3.2.2.21]
Os09t0101100-01  (RAP-DB) Os09g0101100; HhH-GPD domain domain containing protein. [KO:K10801] [EC:3.2.2.-]
Os01t0737300-00  (RAP-DB) Os01g0737300; Similar to Phosphoesterase. [KO:K08073] [EC:3.1.3.32 2.7.1.78]
Os07t0530100-01  (RAP-DB) Os07g0530100; Tyrosyl-DNA phosphodiesterase family protein. [KO:K10862] [EC:3.1.4.-]
Os06t0237200-00  (RAP-DB) Os06g0237200; Similar to DNA polymerase lambda. [KO:K03512] [EC:2.7.7.7 4.2.99.-]
Os07t0413700-01  (RAP-DB) Os07g0413700; Similar to Poly(ADP)-ribose polymerase (EC 2.4.2.30). [KO:K24070] [EC:2.4.2.30]
Os02t0530600-01  (RAP-DB) Os02g0530600; Poly(ADP-ribose) polymerase, regulatory region domain containing protein. [KO:K10798] [EC:2.4.2.30]
Os01t0351100-00  (RAP-DB) Os01g0351100; Similar to Poly. [KO:K10798] [EC:2.4.2.30]
Os01t0351200-00  (RAP-DB) Os01g0351200; Similar to Poly. [KO:K10798] [EC:2.4.2.30]
Os03t0293400-01  (RAP-DB) Os03g0293400; Similar to basic helix-loop-helix family protein. [KO:K10863] [EC:3.6.1.70 3.6.1.71 3.6.1.72]
Os06t0144000-01  (RAP-DB) Os06g0144000; BRCT domain containing protein. [KO:K10803]
Os11t0186400-00  (RAP-DB) Os11g0186400; Similar to DNA polymerase delta catalytic subunit (EC 2.7.7.7). [KO:K02327] [EC:2.7.7.7]
Os03t0128500-01  (RAP-DB) Os03g0128500; Similar to DNA polymerase delta small subunit (EC 2.7.7.7). [KO:K02328]
Os01t0204000-01  (RAP-DB) Os01g0204000; DNA polymerase subunit Cdc27 domain containing protein. [KO:K03504]
Os09t0520100-01  (RAP-DB) Os09g0520100; DNA polymerase delta, subunit 4 family protein. [KO:K03505]
Os08t0163300-00  (RAP-DB) Os08g0163300; Similar to delta DNA polymerase. [KO:K03505]
Os02t0511901-00  (RAP-DB) Os02g0511901; Similar to DNA polymerase. [KO:K02324] [EC:2.7.7.7]
Os05t0160800-01  (RAP-DB) Os05g0160800; Similar to DNA polymerase epsilon subunit 2. [KO:K02325] [EC:2.7.7.7]
Os09t0568200-01  (RAP-DB) Os09g0568200; Similar to DNA polymerase epsilon subunit 3. [KO:K02326] [EC:2.7.7.7]
Os02t0805200-01  (RAP-DB) Os02g0805200; Proliferating cell nuclear antigen (PCNA) (Cyclin). [KO:K04802]
Os11t0572100-01  (RAP-DB) Os11g0572100; Similar to DNA ligase (EC 6.5.1.2). [KO:K10754]
Os12t0176500-01  (RAP-DB) Os12g0176500; Similar to Replication factor C subunit RFC4. [KO:K10755]
Os04t0569000-01  (RAP-DB) Os04g0569000; Similar to Replication factor C 40kDa subunit. [KO:K10755]
Os03t0792600-01  (RAP-DB) Os03g0792600; ATPase, AAA+ type, core domain containing protein. [KO:K10756]
Os10t0574500-00  (RAP-DB) Os10g0574500; DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal domain containing protein. [KO:K10756]
Os02t0775200-01  (RAP-DB) Os02g0775200; Similar to Activator 1 36 kDa subunit (Replication factor C 36 kDa subunit) (A1 36 kDa subunit) (RF-C 36 kDa subunit) (RFC36) (Replication factor C subunit 5). [KO:K10756]
Os05t0540100-01  (RAP-DB) Os05g0540100; Flap endonuclease-1a (EC 3.-.-.-) (OsFEN-1a). [KO:K04799] [EC:3.1.-.-]
Os03t0834000-01  (RAP-DB) Os03g0834000; Flap endonuclease-1b (EC 3.-.-.-) (OsFEN-1b). [KO:K04799] [EC:3.1.-.-]
Os10t0489200-01  (RAP-DB) Os10g0489200; Similar to DNA ligase (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP]). [KO:K10747] [EC:6.5.1.1 6.5.1.6 6.5.1.7]
Os08t0304900-01  (RAP-DB) Os08g0304900; Similar to AtMMH-1 protein (F6D8.28 protein). [KO:K10563] [EC:3.2.2.23 4.2.99.18]
Os06t0643600-01  (RAP-DB) Os06g0643600; DNA glycosylase/AP lyase domain containing protein. [KO:K10563] [EC:3.2.2.23 4.2.99.18]
Os03t0248250-00  (RAP-DB) Os03g0248250; Hypothetical conserved gene. [KO:K01247] [EC:3.2.2.21]
Os05t0567500-01  (RAP-DB) Os05g0567500; HhH-GPD domain domain containing protein. [KO:K01247] [EC:3.2.2.21]
Os05t0579100-01  (RAP-DB) Os05g0579100; HhH-GPD domain domain containing protein. [KO:K01247] [EC:3.2.2.21]
Os01t0799500-01  (RAP-DB) Os01g0799500; Methyladenine glycosylase domain containing protein. [KO:K01246] [EC:3.2.2.20]
Os08t0489300-01  (RAP-DB) Os08g0489300; Methyladenine glycosylase domain containing protein. [KO:K01246] [EC:3.2.2.20]
Os06t0649800-01  (RAP-DB) Os06g0649800; Similar to DNA-3-methyladenine glycosylase I. [KO:K01246] [EC:3.2.2.20]
Os04t0501200-01  (RAP-DB) Os04g0501200; Similar to H0311C03.4 protein. [KO:K01246] [EC:3.2.2.20]
Os09t0420300-01  (RAP-DB) Os09g0420300; Methyladenine glycosylase domain containing protein. [KO:K01246] [EC:3.2.2.20]
Os01t0801000-01  (RAP-DB) Os01g0801000; Similar to Apurinic endonuclease-redox protein (DNA-(apurinic or apyrimidinic site) lyase) (EC 4.2.99.18). [KO:K01142] [EC:3.1.11.2]
Os01t0801100-01  (RAP-DB) Os01g0801100; Similar to Apurinic endonuclease-redox protein (DNA-(apurinic or apyrimidinic site) lyase) (EC 4.2.99.18). [KO:K01142] [EC:3.1.11.2]
Os08t0175300-01  (RAP-DB) Os08g0175300; PolI-like DNA polymerase. [KO:K02335] [EC:2.7.7.7]
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   
LinkDB

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