KEGG   PATHWAY: ccar03420
Entry
ccar03420                   Pathway                                
Name
Nucleotide excision repair - Cyprinus carpio (common carp)
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
ccar03420  Nucleotide excision repair
ccar03420

Other DBs
GO: 0006289
Organism
Cyprinus carpio (common carp) [GN:ccar]
Gene
109076699  rbx1; LOW QUALITY PROTEIN: E3 ubiquitin-protein ligase RBX1 [KO:K03868] [EC:2.3.2.32]
109060319  cullin-4B-like [KO:K10609]
109098133  LOW QUALITY PROTEIN: cullin-4B-like [KO:K10609]
109113043  DNA damage-binding protein 1-like [KO:K10610]
109113065  LOW QUALITY PROTEIN: DNA damage-binding protein 1-like [KO:K10610]
109109984  DNA damage-binding protein 2-like [KO:K10140]
109110490  LOW QUALITY PROTEIN: DNA damage-binding protein 2-like [KO:K10140]
109065409  xpc; DNA repair protein complementing XP-C cells [KO:K10838]
109084464  UV excision repair protein RAD23 homolog B-like isoform X1 [KO:K10839]
109085264  UV excision repair protein RAD23 homolog B-like [KO:K10839]
109076120  UV excision repair protein RAD23 homolog A-like [KO:K10839]
109076121  UV excision repair protein RAD23 homolog A-like [KO:K10839]
109084414  UV excision repair protein RAD23 homolog B-like [KO:K10839]
109102900  centrin-2-like [KO:K10840]
109059122  centrin-2-like [KO:K10840]
109101740  centrin-2-like [KO:K10840]
109105190  DNA excision repair protein ERCC-8-like [KO:K10570]
109109387  LOW QUALITY PROTEIN: DNA excision repair protein ERCC-6-like [KO:K10841]
109062822  LOW QUALITY PROTEIN: UV-stimulated scaffold protein A-like [KO:K23720]
109056007  polr2a; DNA-directed RNA polymerase II subunit RPB1 [KO:K03006] [EC:2.7.7.6]
109067075  DNA-directed RNA polymerase II subunit RPB1-like [KO:K03006] [EC:2.7.7.6]
109046857  LOW QUALITY PROTEIN: DNA-directed RNA polymerase II subunit RPB2-like [KO:K03010] [EC:2.7.7.6]
109050878  DNA-directed RNA polymerase II subunit RPB3-like [KO:K03011]
109050595  polr2c; DNA-directed RNA polymerase II subunit RPB3 [KO:K03011]
109047406  DNA-directed RNA polymerase II subunit RPB4-like [KO:K03012]
109078689  polr2d; DNA-directed RNA polymerase II subunit RPB4 [KO:K03012]
109071198  DNA-directed RNA polymerases I, II, and III subunit RPABC1 [KO:K03013]
109095179  DNA-directed RNA polymerases I, II, and III subunit RPABC1-like isoform X1 [KO:K03013]
109046592  DNA-directed RNA polymerases I, II, and III subunit RPABC1 [KO:K03013]
109061226  polr2f; DNA-directed RNA polymerases I, II, and III subunit RPABC2 [KO:K03014]
109096887  DNA-directed RNA polymerases I, II, and III subunit RPABC2-like [KO:K03014]
109071126  polr2g; DNA-directed RNA polymerase II subunit RPB7 [KO:K03015]
109110454  DNA-directed RNA polymerase II subunit RPB7-like [KO:K03015]
109080980  polr2h; DNA-directed RNA polymerases I, II, and III subunit RPABC3 [KO:K03016]
109059244  polr2i; DNA-directed RNA polymerase II subunit RPB9 [KO:K03017]
109087877  DNA-directed RNA polymerase II subunit RPB9-like [KO:K03017]
109055776  DNA-directed RNA polymerases I, II, and III subunit RPABC4-like [KO:K03009]
109055782  polr2k; DNA-directed RNA polymerases I, II, and III subunit RPABC4 [KO:K03009]
109081995  DNA-directed RNA polymerase II subunit RPB11-a [KO:K03008]
109066872  DNA-directed RNA polymerase II subunit RPB11-a-like [KO:K03008]
109077273  LOW QUALITY PROTEIN: DNA-directed RNA polymerase II subunit GRINL1A-like [KO:K21987]
109113682  DNA-directed RNA polymerase II subunit GRINL1A-like [KO:K21987]
109078831  cyclin-dependent kinase 7 isoform X1 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
109078832  cyclin-dependent kinase 7-like isoform X1 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
109044905  CDK-activating kinase assembly factor MAT1-like [KO:K10842]
109088397  LOW QUALITY PROTEIN: CDK-activating kinase assembly factor MAT1-like [KO:K10842]
109081533  cyclin-H-like isoform X1 [KO:K06634]
109081538  cyclin-H-like [KO:K06634]
109045193  ercc3; TFIIH basal transcription factor complex helicase XPB subunit isoform X1 [KO:K10843] [EC:5.6.2.4]
109084136  ercc2; TFIIH basal transcription factor complex helicase XPD subunit [KO:K10844] [EC:5.6.2.3]
109092384  TFIIH basal transcription factor complex helicase XPD subunit-like isoform X1 [KO:K10844] [EC:5.6.2.3]
109066145  general transcription factor IIH subunit 5-like [KO:K10845]
109051407  general transcription factor IIH subunit 5 [KO:K10845]
109099419  general transcription factor IIH subunit 1-like [KO:K03141]
109098857  LOW QUALITY PROTEIN: general transcription factor IIH subunit 1-like [KO:K03141]
109093947  general transcription factor IIH subunit 2-like [KO:K03142]
109083513  general transcription factor IIH subunit 2 isoform X1 [KO:K03142]
109089153  general transcription factor IIH subunit 2-like [KO:K03142]
109074168  gtf2h3; general transcription factor IIH subunit 3 [KO:K03143]
109098412  gtf2h4; general transcription factor IIH subunit 4 [KO:K03144]
109091027  LOW QUALITY PROTEIN: DNA repair protein complementing XP-G cells homolog [KO:K10846]
109108970  DNA repair protein complementing XP-A cells homolog [KO:K10847]
109056121  rpa1; replication protein A 70 kDa DNA-binding subunit [KO:K07466]
109068204  replication protein A 32 kDa subunit-like [KO:K10739]
109106048  replication protein A 32 kDa subunit-like [KO:K10739]
109106367  replication protein A 32 kDa subunit-A-like [KO:K10739]
109111442  replication protein A 14 kDa subunit-like [KO:K10740]
109111445  replication protein A 14 kDa subunit-like [KO:K10740]
109107672  LOW QUALITY PROTEIN: DNA repair endonuclease XPF-like [KO:K10848] [EC:3.1.-.-]
109078456  LOW QUALITY PROTEIN: DNA excision repair protein ERCC-1-like [KO:K10849]
109086196  DNA excision repair protein ERCC-1-like [KO:K10849]
109095996  ercc1; DNA excision repair protein ERCC-1 [KO:K10849]
109113606  DNA polymerase delta catalytic subunit-like [KO:K02327] [EC:2.7.7.7]
109069549  DNA polymerase delta catalytic subunit-like [KO:K02327] [EC:2.7.7.7]
109079594  DNA polymerase delta catalytic subunit-like [KO:K02327] [EC:2.7.7.7]
109082068  pold2; DNA polymerase delta subunit 2 [KO:K02328]
109096861  DNA polymerase delta subunit 3-like [KO:K03504]
109062048  DNA polymerase delta subunit 3-like [KO:K03504]
109051445  pold4; DNA polymerase delta subunit 4 [KO:K03505]
109079166  DNA polymerase epsilon catalytic subunit A-like [KO:K02324] [EC:2.7.7.7]
109079199  LOW QUALITY PROTEIN: DNA polymerase epsilon catalytic subunit A-like [KO:K02324] [EC:2.7.7.7]
109088633  DNA polymerase epsilon subunit 2-like [KO:K02325] [EC:2.7.7.7]
109093248  pole2; LOW QUALITY PROTEIN: DNA polymerase epsilon subunit 2 [KO:K02325] [EC:2.7.7.7]
109054770  DNA polymerase epsilon subunit 4-like [KO:K03506] [EC:2.7.7.7]
109065206  DNA polymerase epsilon subunit 4-like [KO:K03506] [EC:2.7.7.7]
109110298  proliferating cell nuclear antigen [KO:K04802]
109110302  proliferating cell nuclear antigen-like [KO:K04802]
109089299  LOW QUALITY PROTEIN: replication factor C subunit 1-like [KO:K10754]
109106526  replication factor C subunit 2-like [KO:K10755]
109051737  uncharacterized protein LOC109051737 [KO:K10755]
109108530  replication factor C subunit 2-like [KO:K10755]
109062607  rfc5; replication factor C subunit 5 [KO:K10756]
109068171  replication factor C subunit 5-like [KO:K10756]
109087072  rfc3; replication factor C subunit 3 [KO:K10756]
109108561  LOW QUALITY PROTEIN: DNA ligase 1-like [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
ccar03020  RNA polymerase
ccar04120  Ubiquitin mediated proteolysis
KO pathway
ko03420   
LinkDB

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