ENTRY       sly03420                    Pathway
NAME        Nucleotide excision repair - Solanum lycopersicum (tomato)
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 sly03420  Nucleotide excision repair
DBLINKS     GO: 0006289
ORGANISM    Solanum lycopersicum (tomato) [GN:sly]
GENE        101252794  DNA polymerase I B, chloroplastic/mitochondrial isoform X2 [KO:K02335] [EC:2.7.7.7]
            101249890  RING-box protein 1a [KO:K03868] [EC:2.3.2.32]
            101259644  RING-box protein 1 [KO:K03868] [EC:2.3.2.32]
            101248739  cullin-4 [KO:K10609]
            544135  CUL4; cullin 4 [KO:K10609]
            778355  DDB1; DNA damage-binding protein 1 [KO:K10610]
            101265575  protein DAMAGED DNA-BINDING 2 [KO:K10140]
            101265989  DNA repair protein RAD4 isoform X2 [KO:K10838]
            101258124  ubiquitin receptor RAD23d isoform X1 [KO:K10839]
            101251966  ubiquitin receptor RAD23b isoform X1 [KO:K10839]
            101249452  ubiquitin receptor RAD23c [KO:K10839]
            101246007  RAD23d; ubiquitin receptor RAD23d [KO:K10839]
            101255378  WD repeat-containing protein ATCSA-1-like [KO:K10570]
            101252814  protein CHROMATIN REMODELING 8 [KO:K10841]
            101253215  cyclin-dependent kinase D-3 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            101265536  CDK-activating kinase assembly factor-related [KO:K10842]
            101246966  cyclin-H1-1 [KO:K06634]
            101248768  cyclin-H1-1 isoform X1 [KO:K06634]
            101251406  general transcription and DNA repair factor IIH helicase subunit XPB1 [KO:K10843] [EC:5.6.2.4]
            101255497  general transcription and DNA repair factor IIH helicase subunit XPD [KO:K10844] [EC:5.6.2.3]
            101251518  general transcription and DNA repair factor IIH subunit TFB1-1 isoform X2 [KO:K03141]
            101268093  general transcription factor IIH subunit 2 isoform X1 [KO:K03142]
            101258663  general transcription and DNA repair factor IIH subunit TFB4 [KO:K03143]
            101244148  general transcription and DNA repair factor IIH subunit TFB2 isoform X1 [KO:K03144]
            101260299  DNA repair protein UVH3 isoform X1 [KO:K10846]
            101250913  replication protein A 70 kDa DNA-binding subunit A-like [KO:K07466]
            101259439  replication protein A 70 kDa DNA-binding subunit A [KO:K07466]
            101255870  replication protein A 70 kDa DNA-binding subunit B [KO:K07466]
            101244966  RPA32a; replication protein A [KO:K10739]
            101247082  RPA32b; replication protein A 32 kDa subunit B [KO:K10739]
            101255747  replication protein A 14 kDa subunit B-like isoform X2 [KO:K10740]
            101252714  replication protein A 14 kDa subunit B [KO:K10740]
            101249845  DNA repair endonuclease UVH1 [KO:K10848] [EC:3.1.-.-]
            101261110  DNA excision repair protein ERCC-1 isoform X1 [KO:K10849]
            101256637  DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
            101243681  DNA polymerase delta small subunit [KO:K02328]
            101258997  muscle M-line assembly protein unc-89 [KO:K03504]
            101262116  uncharacterized protein LOC101262116 [KO:K03505]
            101255630  uncharacterized protein LOC101255630 [KO:K03505]
            101253967  DNA polymerase epsilon catalytic subunit A-like isoform X1 [KO:K02324] [EC:2.7.7.7]
            101254462  DNA polymerase epsilon subunit B [KO:K02325] [EC:2.7.7.7]
            101260506  DNA polymerase epsilon subunit 3 [KO:K02326] [EC:2.7.7.7]
            544248  pcna; proliferating cell nuclear antigen [KO:K04802]
            101249468  replication factor C subunit 1 isoform X2 [KO:K10754]
            101268826  replication factor C subunit 2 [KO:K10755]
            101267918  replication factor C subunit 2 [KO:K10755]
            101253010  replication factor C subunit 3 [KO:K10756]
            101250629  replication factor C subunit 3-like isoform X2 [KO:K10756]
            101259119  uncharacterized protein LOC101259119 [KO:K10756]
            101264020  replication factor C subunit 3 [KO:K10756]
            101262281  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 sly03020  RNA polymerase
            sly04120  Ubiquitin mediated proteolysis
KO_PATHWAY  ko03420
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