KEGG   PATHWAY: ogo03420
Entry
ogo03420                    Pathway                                
Name
Nucleotide excision repair - Oncorhynchus gorbuscha (pink salmon)
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
ogo03420  Nucleotide excision repair
ogo03420

Other DBs
GO: 0006289
Organism
Oncorhynchus gorbuscha (pink salmon) [GN:ogo]
Gene
123990716  polr2j; LOW QUALITY PROTEIN: DNA-directed RNA polymerase II subunit RPB11-a [KO:K03008]
123991081  polr2h; DNA-directed RNA polymerases I, II, and III subunit RPABC3 [KO:K03016]
123992271  [KO:K03017]
123992728  [KO:K07466]
123992836  polr2d; DNA-directed RNA polymerase II subunit RPB4 [KO:K03012]
123993440  [KO:K03010] [EC:2.7.7.6]
123993537  [KO:K10609]
123993685  [KO:K10840]
123993726  pold3; DNA polymerase delta subunit 3 isoform X1 [KO:K03504]
123993757  [KO:K03015]
123993966  ercc2; general transcription and DNA repair factor IIH helicase subunit XPD isoform X1 [KO:K10844] [EC:5.6.2.3]
123994099  cetn4; caltractin [KO:K10840]
123995225  gtf2h5; general transcription factor IIH subunit 5 [KO:K10845]
123995226  rfc3; LOW QUALITY PROTEIN: replication factor C subunit 3 [KO:K10756]
123996933  [KO:K10755]
123997150  [KO:K10839]
123997576  [KO:K10739]
123998578  [KO:K03014]
123998762  rad23ab; RAD23 homolog A, nucleotide excision repair protein b [KO:K10839]
123998939  pole4; DNA polymerase epsilon subunit 4 [KO:K03506] [EC:2.7.7.7]
123998978  [KO:K10839]
123999096  polr2eb; DNA-directed RNA polymerases I, II, and III subunit RPABC1 [KO:K03013]
123999496  [KO:K10839]
123999913  [KO:K03008]
123999921  polr2c; DNA-directed RNA polymerase II subunit RPB3 [KO:K03011]
124000287  [KO:K03868] [EC:2.3.2.32]
124001745  pole2; DNA polymerase epsilon subunit 2 isoform X1 [KO:K02325] [EC:2.7.7.7]
124002035  pold4; LOW QUALITY PROTEIN: DNA polymerase delta subunit 4 [KO:K03505]
124004627  polr2i; DNA-directed RNA polymerase II subunit RPB9 [KO:K03017]
124004844  rpa2; replication protein A 32 kDa subunit [KO:K10739]
124005678  [KO:K07466]
124007827  [KO:K03006] [EC:2.7.7.6]
124009810  lig1; LOW QUALITY PROTEIN: DNA ligase 1 [KO:K10747] [EC:6.5.1.1 6.5.1.6 6.5.1.7]
124010536  polr2g; DNA-directed RNA polymerase II subunit RPB7 [KO:K03015]
124010823  [KO:K03010] [EC:2.7.7.6]
124010936  uvssa; UV-stimulated scaffold protein A [KO:K23720]
124011402  [KO:K10840]
124011679  [KO:K10609]
124011721  rfc2; replication factor C subunit 2 isoform X1 [KO:K10755]
124012654  [KO:K10740]
124012825  [KO:K10847]
124012833  [KO:K03009]
124013576  [KO:K03006] [EC:2.7.7.6]
124015619  [KO:K03014]
124015661  [KO:K03868] [EC:2.3.2.32]
124017146  [KO:K10847]
124018303  [KO:K10846]
124018315  [KO:K10846]
124018718  [KO:K10843] [EC:5.6.2.4]
124019629  [KO:K10839]
124023159  [KO:K10846]
124023381  [KO:K10609]
124024854  rfc1; replication factor C subunit 1 isoform X1 [KO:K10754]
124026226  [KO:K02327] [EC:2.7.7.7]
124027425  [KO:K10754]
124028086  [KO:K02327] [EC:2.7.7.7]
124028727  [KO:K10609]
124030766  [KO:K02328]
124031333  ercc1; DNA excision repair protein ERCC-1 [KO:K10849]
124031764  xpc; DNA repair protein complementing XP-C cells [KO:K10838]
124033274  cdk7; cyclin-dependent kinase 7 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
124033301  gtf2h3; general transcription factor IIH subunit 3 isoform X1 [KO:K03143]
124033643  [KO:K03007]
124033739  [KO:K21987]
124033937  [KO:K10610]
124034195  [KO:K04802]
124035050  [KO:K21987]
124035260  ercc8; DNA excision repair protein ERCC-8 isoform X1 [KO:K10570]
124035627  [KO:K03007]
124035910  [KO:K10610]
124036011  ccnh; cyclin-H isoform X1 [KO:K06634]
124036039  pole; DNA polymerase epsilon catalytic subunit A [KO:K02324] [EC:2.7.7.7]
124036453  [KO:K04802]
124036538  pold2; DNA polymerase delta subunit 2 [KO:K02328]
124036588  [KO:K10756]
124036634  gtf2h2; general transcription factor IIH subunit 2 isoform X1 [KO:K03142]
124036968  ddb2; DNA damage-binding protein 2 [KO:K10140]
124037465  gtf2h1; general transcription factor IIH subunit 1 [KO:K03141]
124037786  [KO:K10755]
124039310  ercc4; LOW QUALITY PROTEIN: DNA repair endonuclease XPF [KO:K10848] [EC:3.1.-.-]
124041476  ercc6; DNA excision repair protein ERCC-6 [KO:K10841]
124042633  [KO:K03009]
124043146  gtf2h4; general transcription factor IIH subunit 4 [KO:K03144]
124043343  [KO:K10740]
124046520  mnat1; CDK-activating kinase assembly factor MAT1 isoform X1 [KO:K10842]
124047958  pole3; DNA polymerase epsilon subunit 3 [KO:K02326] [EC:2.7.7.7]
124048554  [KO:K10839]
Reference
  Authors
Sugasawa K.
  Title
[Molecular mechanism of mammalian nucleotide excision repair]
  Journal
Tanpakushitsu Kakusan Koso 46:893-901 (2001)
Reference
  Authors
Nakatsu Y.
  Title
[Transcription-coupled repair and Cockayne syndrome]
  Journal
Tanpakushitsu Kakusan Koso 46:908-15 (2001)
Reference
  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
  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
  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
  Authors
Sugasawa K.
  Title
[DNA repair pathways involving Cul4A ubiquitin ligases]
  Journal
Tanpakushitsu Kakusan Koso 51:1339-44 (2006)
Reference
  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
ogo03020  RNA polymerase
ogo04120  Ubiquitin mediated proteolysis
KO pathway
ko03420   

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