KEGG   PATHWAY: osa03420
Entry
osa03420                    Pathway                                
Name
Nucleotide excision repair - Oryza sativa japonica (Japanese rice)
Description
Nucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the NER pathway are linked to at least three diseases: xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). The repair of damaged DNA involves at least 30 polypeptides within two different sub-pathways of NER known as transcription-coupled repair (TCR-NER) and global genome repair (GGR-NER). TCR refers to the expedited repair of lesions located in the actively transcribed strand of genes by RNA polymerase II (RNAP II). In GGR-NER the first step of damage recognition involves XPC-hHR23B complex together with XPE complex (in prokaryotes, uvrAB complex). The following steps of GGR-NER and TCR-NER are similar.
Class
Genetic Information Processing; Replication and repair
Pathway map
osa03420  Nucleotide excision repair
osa03420

Other DBs
GO: 0006289
Organism
Oryza sativa japonica (Japanese rice) [GN:osa]
Gene
4337150  DNA polymerase I A, chloroplastic-like isoform X1 [KO:K02335] [EC:2.7.7.7]
4344789  OsJ_26226; DNA polymerase I A, chloroplastic [KO:K02335] [EC:2.7.7.7]
4344791  DNA polymerase I B, mitochondrial isoform 1 [KO:K02335] [EC:2.7.7.7]
4326152  RING-box protein 1A [KO:K03868] [EC:2.3.2.32]
4330476  uncharacterized protein [KO:K03868] [EC:2.3.2.32]
4334354  cullin-4 [KO:K10609]
4339794  DBB1; DNA damage-binding protein 1 isoform 1 [KO:K10610]
4325482  DNA damage-binding protein 2-like [KO:K10140]
4345619  DNA repair protein RAD4 [KO:K10838]
4328500  ubiquitin receptor RAD23b [KO:K10839]
4345632  probable ubiquitin receptor RAD23 isoform X1 [KO:K10839]
4347014  OsJ_29306; probable ubiquitin receptor RAD23 isoform 1 [KO:K10839]
4340699  ubiquitin receptor RAD23d [KO:K10839]
4329118  WD repeat-containing protein ATCSA-1 isoform X1 [KO:K10570]
4324761  WD repeat-containing protein ATCSA-1 isoform X1 [KO:K10570]
4326441  CSB; DNA excision repair protein CSB [KO:K10841]
4326574  SNF2 domain-containing protein ENL1-like isoform X1 [KO:K10841]
4329068  UV-stimulated scaffold protein A homolog isoform X1 [KO:K23720]
4337831  DNA-directed RNA polymerase II subunit RPB1 [KO:K03006] [EC:2.7.7.6]
9267835  DNA-directed RNA polymerase II subunit RPB1 [KO:K03006] [EC:2.7.7.6]
136351388  DNA-directed RNA polymerase II subunit RPB1-like [KO:K03006] [EC:2.7.7.6]
4333571  DNA-directed RNA polymerase II subunit RPB2 [KO:K03010] [EC:2.7.7.6]
4346392  DNA-directed RNA polymerases II, IV and V subunit 3 [KO:K03011]
4328083  DNA-directed RNA polymerase II subunit 4 [KO:K03012]
4330570  DNA-directed RNA polymerase II subunit 4 [KO:K03012]
4327549  DNA-directed RNA polymerases II and IV subunit 5A [KO:K03013]
9270850  DNA-directed RNA polymerases II and IV subunit 5A [KO:K03013]
4349748  DNA-directed RNA polymerase V subunit 5A [KO:K03013]
4351463  DNA-directed RNA polymerase V subunit 5A [KO:K03013]
4343168  DNA-directed RNA polymerases II, IV and V subunit 6A [KO:K03014]
4333343  DNA-directed RNA polymerases II, IV and V subunit 6A [KO:K03014]
4338726  DNA-directed RNA polymerase II subunit RPB7 [KO:K03015]
4334766  DNA-directed RNA polymerases II, IV and V subunit 8B [KO:K03016]
4341946  DNA-directed RNA polymerases II, IV and V subunit 8B [KO:K03016]
4352511  DNA-directed RNA polymerases II, IV and V subunit 9B [KO:K03017]
4331295  DNA-directed RNA polymerases II, IV and V subunit 9B [KO:K03017]
4343902  DNA-directed RNA polymerases II, IV and V subunit 9A isoform X1 [KO:K03017]
4349985  DNA-directed RNA polymerases I, II, and III subunit RPABC5 [KO:K03007]
4351671  DNA-directed RNA polymerases I, II, and III subunit RPABC5 [KO:K03007]
9272152  DNA-directed RNA polymerases II, IV and V subunit 12 [KO:K03009]
9269422  DNA-directed RNA polymerases II, IV and V subunit 12 [KO:K03009]
136357350  DNA-directed RNA polymerases II, IV and V subunit 12-like [KO:K03009]
4342517  DNA-directed RNA polymerases II, IV and V subunit 11 isoform X2 [KO:K03008]
4338689  CAK-R2; cyclin-dependent kinase D-1 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
4340268  uncharacterized LOC4340268 [KO:K10842]
4350497  uncharacterized protein [KO:K10842]
4334040  CYCH-1; cyclin-H1-1 [KO:K06634]
4325640  general transcription and DNA repair factor IIH helicase/translocase subunit XPB1 [KO:K10843] [EC:5.6.2.4]
4337788  general transcription and DNA repair factor IIH helicase subunit XPD [KO:K10844] [EC:5.6.2.3]
4343686  general transcription and DNA repair factor IIH subunit TFB5 [KO:K10845]
4338052  general transcription and DNA repair factor IIH subunit TFB5 [KO:K10845]
4345313  general transcription and DNA repair factor IIH subunit TFB1-1 [KO:K03141]
4336358  general transcription factor IIH subunit 2 [KO:K03142]
4328152  general transcription and DNA repair factor IIH subunit TFB4 [KO:K03143]
4337426  general transcription and DNA repair factor IIH subunit TFB2 isoform X1 [KO:K03144]
4331991  DNA repair protein UVH3 isoform X1 [KO:K10846]
4337594  OsJ_16860; replication protein A 70 kDa DNA-binding subunit C [KO:K07466]
4330902  OsJ_08582; replication protein A 70 kDa DNA-binding subunit A [KO:K07466]
4332052  OsJ_09906; replication protein A 70 kDa DNA-binding subunit B [KO:K07466]
4331236  OsJ_08977; replication protein A 32 kDa subunit A [KO:K10739]
4330068  OsRPA32-2; replication protein A 32 kDa subunit B [KO:K10739]
4327706  OsJ_01130; replication protein A 14 kDa subunit isoform X2 [KO:K10740]
4331279  DNA repair endonuclease UVH1 [KO:K10848] [EC:3.1.-.-]
4349131  DNA excision repair protein ERCC-1 [KO:K10849]
4349968  OspolD1; DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
4331489  OJ1528D07.1; DNA polymerase delta small subunit [KO:K02328]
4327080  uncharacterized protein [KO:K03504]
4347604  P0669G04.6; uncharacterized LOC4347604 [KO:K03505]
4344737  uncharacterized protein [KO:K03505]
112936215  uncharacterized protein [KO:K03505]
4329458  DNA polymerase epsilon catalytic subunit A [KO:K02324] [EC:2.7.7.7]
4337886  DNA polymerase epsilon subunit B [KO:K02325] [EC:2.7.7.7]
4347894  DNA polymerase II subunit B4 [KO:K02326] [EC:2.7.7.7]
4331062  Cyclin; proliferating cell nuclear antigen [KO:K04802]
4350754  OsRFC1; replication factor C subunit 1 [KO:K10754]
4351654  OsJ_35406; replication factor C subunit 2 [KO:K10755]
4336704  OsRFC4; replication factor C subunit 4 [KO:K10755]
4330895  OsRFC3; replication factor C subunit 3 [KO:K10756]
4334389  OsJ_12910; replication factor C subunit 5 [KO:K10756]
4349480  replication factor C subunit 3 [KO:K10756]
4348965  DNA ligase 1 isoform X1 [KO:K10747] [EC:6.5.1.1 6.5.1.6 6.5.1.7]
Reference
PMID:11436314
  Authors
Sugasawa K.
  Title
[Molecular mechanism of mammalian nucleotide excision repair]
  Journal
Tanpakushitsu Kakusan Koso 46:893-901 (2001)
Reference
PMID:11436316
  Authors
Nakatsu Y.
  Title
[Transcription-coupled repair and Cockayne syndrome]
  Journal
Tanpakushitsu Kakusan Koso 46:908-15 (2001)
Reference
PMID:11436323
  Authors
Nakagawa N, Masui R, Kuramitsu S.
  Title
[Structure and function of DNA repair enzyme UvrB from Thermus thermophilus HB8]
  Journal
Tanpakushitsu Kakusan Koso 46:968-75 (2001)
Reference
PMID:17276014
  Authors
Kraemer KH, Patronas NJ, Schiffmann R, Brooks BP, Tamura D, DiGiovanna JJ.
  Title
Xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome: a complex genotype-phenotype relationship.
  Journal
Neuroscience 145:1388-96 (2007)
DOI:10.1016/j.neuroscience.2006.12.020
Reference
PMID:17884153
  Authors
Saldivar JS, Wu X, Follen M, Gershenson D.
  Title
Nucleotide excision repair pathway review I: implications in ovarian cancer and platinum sensitivity.
  Journal
Gynecol Oncol 107:S56-71 (2007)
DOI:10.1016/j.ygyno.2007.07.043
Reference
PMID:16922398
  Authors
Sugasawa K.
  Title
[DNA repair pathways involving Cul4A ubiquitin ligases]
  Journal
Tanpakushitsu Kakusan Koso 51:1339-44 (2006)
Reference
PMID:18018633
  Authors
Ito S, Ando D, Tanaka K.
  Title
[Cross-talk between DNA repair and transcription: molecular mechanism and disorders]
  Journal
Tanpakushitsu Kakusan Koso 52:1823-31 (2007)
Related
pathway
osa03020  RNA polymerase
osa04120  Ubiquitin mediated proteolysis
KO pathway
ko03420   
LinkDB

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