KEGG   PATHWAY: otw03420
Entry
otw03420                    Pathway                                
Name
Nucleotide excision repair - Oncorhynchus tshawytscha (Chinook 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
otw03420  Nucleotide excision repair
otw03420

Other DBs
GO: 0006289
Organism
Oncorhynchus tshawytscha (Chinook salmon) [GN:otw]
Gene
112226161  RING-box protein 1 [KO:K03868] [EC:2.3.2.32]
112258810  RING-box protein 1 [KO:K03868] [EC:2.3.2.32]
112247600  RING-box protein 1-like [KO:K03868] [EC:2.3.2.32]
112221086  cullin-4B isoform X1 [KO:K10609]
112256372  cullin-4B isoform X1 [KO:K10609]
112263480  DNA damage-binding protein 1 [KO:K10610]
112248982  DNA damage-binding protein 1 isoform X1 [KO:K10610]
112241207  ddb2; DNA damage-binding protein 2 isoform X1 [KO:K10140]
112258278  xpc; DNA repair protein complementing XP-C cells [KO:K10838]
112250788  UV excision repair protein RAD23 homolog B [KO:K10839]
112258729  UV excision repair protein RAD23 homolog A [KO:K10839]
112258840  rad23aa; UV excision repair protein RAD23 homolog A isoform X1 [KO:K10839]
112252189  UV excision repair protein RAD23 homolog B isoform X1 [KO:K10839]
112219608  rad23b; UV excision repair protein RAD23 homolog B isoform X1 [KO:K10839]
112257367  UV excision repair protein RAD23 homolog B [KO:K10839]
112221227  cetn2; caltractin [KO:K10840]
112262636  ercc8; DNA excision repair protein ERCC-8 isoform X1 [KO:K10570]
112253510  ercc6; DNA excision repair protein ERCC-6 isoform X1 [KO:K10841]
112256009  uvssa; UV-stimulated scaffold protein A isoform X1 [KO:K23720]
112260051  LOW QUALITY PROTEIN: DNA-directed RNA polymerase II subunit RPB1-like [KO:K03006] [EC:2.7.7.6]
112214767  DNA-directed RNA polymerase II subunit RPB1-like [KO:K03006] [EC:2.7.7.6]
112220984  DNA-directed RNA polymerase II subunit RPB2 isoform X1 [KO:K03010] [EC:2.7.7.6]
112256269  DNA-directed RNA polymerase II subunit RPB2-like [KO:K03010] [EC:2.7.7.6]
112252283  polr2c; DNA-directed RNA polymerase II subunit RPB3 isoform X1 [KO:K03011]
112238832  DNA-directed RNA polymerase II subunit RPB4 [KO:K03012]
112234011  polr2d; DNA-directed RNA polymerase II subunit RPB4 [KO:K03012]
112260793  DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform X1 [KO:K03013]
112252226  polr2eb; DNA-directed RNA polymerases I, II, and III subunit RPABC1 [KO:K03013]
112226160  DNA-directed RNA polymerases I, II, and III subunit RPABC2 [KO:K03014]
112258772  DNA-directed RNA polymerases I, II, and III subunit RPABC2 isoform X1 [KO:K03014]
112221281  DNA-directed RNA polymerase II subunit RPB7 [KO:K03015]
112234833  DNA-directed RNA polymerase II subunit RPB7 [KO:K03015]
112253288  polr2h; DNA-directed RNA polymerases I, II, and III subunit RPABC3 [KO:K03016]
112267176  polr2i; DNA-directed RNA polymerase II subunit RPB9 [KO:K03017]
112247043  DNA-directed RNA polymerases I, II, and III subunit RPABC5 isoform X1 [KO:K03007]
112263813  DNA-directed RNA polymerases I, II, and III subunit RPABC5 [KO:K03007]
112236595  polr2k; DNA-directed RNA polymerases I, II, and III subunit RPABC4 [KO:K03009]
112257932  polr2j; DNA-directed RNA polymerase II subunit RPB11-a [KO:K03008]
112263720  polr2m; LOW QUALITY PROTEIN: protein GRINL1A [KO:K21987]
112248573  cdk7; cyclin-dependent kinase 7 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
112256765  mnat1; CDK-activating kinase assembly factor MAT1 isoform X1 [KO:K10842]
112263374  ccnh; cyclin-H isoform X1 [KO:K06634]
121844506  LOW QUALITY PROTEIN: general transcription and DNA repair factor IIH helicase subunit XPB-like [KO:K10843] [EC:5.6.2.4]
112265301  ercc2; general transcription and DNA repair factor IIH helicase subunit XPD [KO:K10844] [EC:5.6.2.3]
112217727  gtf2h5; general transcription factor IIH subunit 5 [KO:K10845]
112242150  gtf2h1; general transcription factor IIH subunit 1 [KO:K03141]
112262528  gtf2h2; general transcription factor IIH subunit 2 isoform X1 [KO:K03142]
112245944  gtf2h3; general transcription factor IIH subunit 3 [KO:K03143]
112229405  gtf2h4; general transcription factor IIH subunit 4 [KO:K03144]
112232428  DNA repair protein complementing XP-A cells homolog [KO:K10847]
112231838  DNA repair protein complementing XP-A cells homolog [KO:K10847]
112267112  rpa1; replication protein A 70 kDa DNA-binding subunit isoform X1 [KO:K07466]
112265533  replication protein A 70 kDa DNA-binding subunit isoform X1 [KO:K07466]
112223102  replication protein A 32 kDa subunit [KO:K10739]
112264614  replication protein A 32 kDa subunit-like [KO:K10739]
112246531  rpa2; replication protein A 32 kDa subunit [KO:K10739]
112264588  rpa3; replication protein A 14 kDa subunit [KO:K10740]
112229607  replication protein A 14 kDa subunit [KO:K10740]
112224420  ercc4; LOW QUALITY PROTEIN: DNA repair endonuclease XPF [KO:K10848] [EC:3.1.-.-]
112225671  ercc1; DNA excision repair protein ERCC-1 [KO:K10849]
112238545  pold1; DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
112262622  pold2; DNA polymerase delta subunit 2 [KO:K02328]
112228871  pold3; DNA polymerase delta subunit 3 isoform X1 [KO:K03504]
112261376  pold4; DNA polymerase delta subunit 4 [KO:K03505]
112263293  pole; DNA polymerase epsilon catalytic subunit A [KO:K02324] [EC:2.7.7.7]
112262096  pole2; DNA polymerase epsilon subunit 2 isoform X1 [KO:K02325] [EC:2.7.7.7]
112220048  pole3; DNA polymerase epsilon subunit 3 [KO:K02326] [EC:2.7.7.7]
112251792  DNA polymerase epsilon subunit 4 isoform X1 [KO:K03506] [EC:2.7.7.7]
112252208  pole4; DNA polymerase epsilon subunit 4 [KO:K03506] [EC:2.7.7.7]
112248619  proliferating cell nuclear antigen [KO:K04802]
112262735  proliferating cell nuclear antigen [KO:K04802]
112237891  LOW QUALITY PROTEIN: replication factor C subunit 1 [KO:K10754]
112251032  replication factor C subunit 4 isoform X1 [KO:K10755]
112248321  replication factor C subunit 4 isoform X1 [KO:K10755]
112228475  rfc2; replication factor C subunit 2 isoform X1 [KO:K10755]
112239162  rfc3; replication factor C subunit 3 [KO:K10756]
112262561  rfc5; replication factor C subunit 5 [KO:K10756]
112236506  lig1; 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)
Related
pathway
otw03020  RNA polymerase
otw04120  Ubiquitin mediated proteolysis
KO pathway
ko03420   
LinkDB

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