KEGG   PATHWAY: aof03420
Entry
aof03420                    Pathway                                
Name
Nucleotide excision repair - Asparagus officinalis (garden asparagus)
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
aof03420  Nucleotide excision repair
aof03420

Other DBs
GO: 0006289
Organism
Asparagus officinalis (garden asparagus) [GN:aof]
Gene
109822202  DNA polymerase I A, chloroplastic-like isoform X1 [KO:K02335] [EC:2.7.7.7]
109828983  RING-box protein 1a-like [KO:K03868] [EC:2.3.2.32]
109844953  RING-box protein 1a [KO:K03868] [EC:2.3.2.32]
109846322  LOW QUALITY PROTEIN: cullin-4-like [KO:K10609]
109848632  LOW QUALITY PROTEIN: cullin-4-like [KO:K10609]
109825984  DNA damage-binding protein 1a [KO:K10610]
109821912  DNA damage-binding protein 2-like [KO:K10140]
109837752  DNA damage-binding protein 2 isoform X1 [KO:K10140]
109844610  DNA repair protein RAD4 isoform X1 [KO:K10838]
109842304  ubiquitin receptor RAD23b-like [KO:K10839]
109841292  ubiquitin receptor RAD23b [KO:K10839]
109845025  LOW QUALITY PROTEIN: ubiquitin receptor RAD23b-like [KO:K10839]
109844419  LOW QUALITY PROTEIN: ubiquitin receptor RAD23d-like [KO:K10839]
109849310  ubiquitin receptor RAD23d-like [KO:K10839]
109850270  ubiquitin receptor RAD23d-like [KO:K10839]
109825496  DNA excision repair protein ERCC-8-like [KO:K10570]
109823626  DNA excision repair protein CSB [KO:K10841]
109822418  LOW QUALITY PROTEIN: UV-stimulated scaffold protein A homolog [KO:K23720]
109827408  DNA-directed RNA polymerase II subunit 1 [KO:K03006] [EC:2.7.7.6]
109839540  DNA-directed RNA polymerase II subunit RPB2 [KO:K03010] [EC:2.7.7.6]
109841114  DNA-directed RNA polymerases II, IV and V subunit 3-like [KO:K03011]
109819980  DNA-directed RNA polymerases IV and V subunit 4-like isoform X1 [KO:K03012]
109837638  DNA-directed RNA polymerase II subunit 4 [KO:K03012]
109829039  DNA-directed RNA polymerase V subunit 5A-like [KO:K03013]
109830532  DNA-directed RNA polymerases II and IV subunit 5A-like [KO:K03013]
109831692  DNA-directed RNA polymerases II and IV subunit 5A [KO:K03013]
109825382  DNA-directed RNA polymerases II, IV and V subunit 6A-like [KO:K03014]
109835422  DNA-directed RNA polymerase II subunit RPB7-like [KO:K03015]
109850380  DNA-directed RNA polymerase II subunit RPB7 [KO:K03015]
109832463  DNA-directed RNA polymerases II and V subunit 8A-like [KO:K03016]
109820641  DNA-directed RNA polymerases II, IV and V subunit 9B-like isoform X1 [KO:K03017]
109850844  DNA-directed RNA polymerases II, IV and V subunit 9A [KO:K03017]
109824707  DNA-directed RNA polymerases I, II, and III subunit RPABC5-like [KO:K03007]
109830304  DNA-directed RNA polymerases I, II, and III subunit RPABC5 [KO:K03007]
109822285  DNA-directed RNA polymerases II, IV and V subunit 12 [KO:K03009]
109830164  DNA-directed RNA polymerases II, IV and V subunit 11-like [KO:K03008]
109834585  DNA-directed RNA polymerases II, IV and V subunit 11-like [KO:K03008]
109848719  cyclin-dependent kinase D-1-like [KO:K02202] [EC:2.7.11.22 2.7.11.23]
109830469  LOW QUALITY PROTEIN: uncharacterized protein LOC109830469 [KO:K10842]
109827778  LOW QUALITY PROTEIN: cyclin-H1-1-like [KO:K06634]
109840114  cyclin-H1-1-like [KO:K06634]
109823652  DNA repair helicase XPB1-like [KO:K10843] [EC:5.6.2.4]
109845381  DNA repair helicase XPB1 isoform X1 [KO:K10843] [EC:5.6.2.4]
109831389  LOW QUALITY PROTEIN: DNA repair helicase XPD [KO:K10844] [EC:5.6.2.3]
109822475  RNA polymerase II transcription factor B subunit 5 isoform X1 [KO:K10845]
109848274  probable RNA polymerase II transcription factor B subunit 1-1 [KO:K03141]
109837187  general transcription factor IIH subunit 2 [KO:K03142]
109850653  RNA polymerase II transcription factor B subunit 4-like isoform X1 [KO:K03143]
109825191  RNA polymerase II transcription factor B subunit 2 isoform X1 [KO:K03144]
109826468  RNA polymerase II transcription factor B subunit 2-like [KO:K03144]
109850458  DNA repair protein UVH3 [KO:K10846]
109848350  LOW QUALITY PROTEIN: replication protein A 70 kDa DNA-binding subunit A-like [KO:K07466]
109844619  replication protein A 70 kDa DNA-binding subunit A [KO:K07466]
109849301  replication protein A 70 kDa DNA-binding subunit B [KO:K07466]
109840439  replication protein A 32 kDa subunit A-like [KO:K10739]
109850670  replication protein A 32 kDa subunit A-like [KO:K10739]
109837420  replication protein A 32 kDa subunit B-like [KO:K10739]
109822023  replication protein A 14 kDa subunit-like [KO:K10740]
109839311  DNA repair endonuclease UVH1 [KO:K10848] [EC:3.1.-.-]
109839562  DNA excision repair protein ERCC-1 [KO:K10849]
109823232  DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
109836584  DNA polymerase delta small subunit [KO:K02328]
109825967  uncharacterized protein LOC109825967 [KO:K03504]
109825400  DNA polymerase delta subunit 4 [KO:K03505]
109823749  DNA polymerase epsilon catalytic subunit A isoform X1 [KO:K02324] [EC:2.7.7.7]
109846470  DNA polymerase epsilon subunit B-like isoform X1 [KO:K02325] [EC:2.7.7.7]
109821994  proliferating cell nuclear antigen-like [KO:K04802]
109850145  proliferating cell nuclear antigen [KO:K04802]
109843874  replication factor C subunit 1 isoform X1 [KO:K10754]
109838651  replication factor C subunit 2 [KO:K10755]
109837963  LOW QUALITY PROTEIN: replication factor C subunit 2 [KO:K10755]
109832946  replication factor C subunit 3 [KO:K10756]
109837436  replication factor C subunit 3-like [KO:K10756]
109845383  LOW QUALITY PROTEIN: replication factor C subunit 3 [KO:K10756]
109844293  uncharacterized protein LOC109844293 isoform X1 [KO:K10756]
109837785  DNA ligase 1-like 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
aof03020  RNA polymerase
aof04120  Ubiquitin mediated proteolysis
KO pathway
ko03420   
LinkDB

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