ENTRY       osa03420                    Pathway
NAME        Nucleotide excision repair - Oryza sativa japonica (Japanese rice) (RefSeq)
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
DBLINKS     GO: 0006289
ORGANISM    Oryza sativa japonica (Japanese rice) (RefSeq) [GN:osa]
GENE        4337150  DNA polymerase I A, chloroplastic-like isoform X1 [KO:K02335] [EC:2.7.7.7]
            4344789  DNA polymerase I A, chloroplastic [KO:K02335] [EC:2.7.7.7]
            4326152  RING-box protein 1a [KO:K03868] [EC:2.3.2.32]
            4330476  RING-box protein 1 [KO:K03868] [EC:2.3.2.32]
            4334354  cullin-4 [KO:K10609]
            4339794  DNA damage-binding protein 1a isoform X1 [KO:K10610]
            4325482  protein DAMAGED DNA-BINDING 2 [KO:K10140]
            4345619  DNA repair protein RAD4 [KO:K10838]
            4328500  ubiquitin receptor RAD23b isoform X1 [KO:K10839]
            4345632  probable ubiquitin receptor RAD23 isoform X1 [KO:K10839]
            4347014  probable ubiquitin receptor RAD23 isoform X3 [KO:K10839]
            4340699  ubiquitin receptor RAD23d [KO:K10839]
            4329118  DNA excision repair protein ERCC-8 isoform X1 [KO:K10570]
            4324761  DNA excision repair protein ERCC-8 isoform X1 [KO:K10570]
            4326441  protein CHROMATIN REMODELING 8 [KO:K10841]
            4326574  protein CHROMATIN REMODELING 24 isoform X1 [KO:K10841]
            4338689  cyclin-dependent kinase D-1 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            4340268  uncharacterized protein LOC4340268 [KO:K10842]
            4350497  uncharacterized protein LOC4350497 [KO:K10842]
            4334040  cyclin-H1-1 isoform X1 [KO:K06634]
            4325640  DNA repair helicase XPB1 [KO:K10843] [EC:5.6.2.4]
            4337788  DNA repair helicase UVH6 [KO:K10844] [EC:5.6.2.3]
            4343686  general transcription factor IIH subunit 5 [KO:K10845]
            4338052  general transcription factor IIH subunit 5 [KO:K10845]
            4345313  probable RNA polymerase II transcription factor B subunit 1-1 isoform X1 [KO:K03141]
            4336358  general transcription factor IIH subunit 2 [KO:K03142]
            4328152  general transcription factor IIH subunit 3 [KO:K03143]
            4337426  general transcription factor IIH subunit 4 [KO:K03144]
            4331991  DNA repair protein UVH3 isoform X1 [KO:K10846]
            4337594  replication protein A 70 kDa DNA-binding subunit C [KO:K07466]
            4330902  replication protein A 70 kDa DNA-binding subunit A [KO:K07466]
            4332052  replication protein A 70 kDa DNA-binding subunit B [KO:K07466]
            4331236  replication protein A 32 kDa subunit A [KO:K10739]
            4330068  replication protein A 32 kDa subunit B isoform X2 [KO:K10739]
            4327706  replication protein A 14 kDa subunit [KO:K10740]
            4331279  DNA repair endonuclease UVH1 [KO:K10848] [EC:3.1.-.-]
            4349131  DNA excision repair protein ERCC-1 [KO:K10849]
            4349968  DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
            4331489  DNA polymerase delta small subunit [KO:K02328]
            4327080  protein IWS1 homolog A [KO:K03504]
            4347604  uncharacterized protein LOC4347604 [KO:K03505]
            4344737  DNA polymerase delta subunit 4 [KO:K03505]
            4329458  DNA polymerase epsilon catalytic subunit A isoform X1 [KO:K02324] [EC:2.7.7.7]
            4337886  DNA polymerase epsilon subunit 2 [KO:K02325] [EC:2.7.7.7]
            4347894  DNA polymerase epsilon subunit 3 [KO:K02326] [EC:2.7.7.7]
            4331062  proliferating cell nuclear antigen [KO:K04802]
            4350754  replication factor C subunit 1 [KO:K10754]
            4351654  replication factor C subunit 2 [KO:K10755]
            4336704  replication factor C subunit 4 [KO:K10755]
            4330895  replication factor C subunit 3 [KO:K10756]
            4334389  replication factor C subunit 5 [KO:K10756]
            4349480  replication factor C subunit 3 [KO:K10756]
            4348965  DNA ligase 1 [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)
REL_PATHWAY osa03020  RNA polymerase
            osa04120  Ubiquitin mediated proteolysis
KO_PATHWAY  ko03420
///
