ENTRY       gmx03420                    Pathway
NAME        Nucleotide excision repair - Glycine max (soybean)
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 gmx03420  Nucleotide excision repair
DBLINKS     GO: 0006289
ORGANISM    Glycine max (soybean) [GN:gmx]
GENE        100797016  DNA polymerase I A, chloroplastic/mitochondrial [KO:K02335] [EC:2.7.7.7]
            100807239  DNA polymerase I A, chloroplastic/mitochondrial [KO:K02335] [EC:2.7.7.7]
            100790704  DNA polymerase I B, chloroplastic/mitochondrial isoform X1 [KO:K02335] [EC:2.7.7.7]
            100500045  uncharacterized protein LOC100500045 [KO:K03868] [EC:2.3.2.32]
            100789570  RING-box protein 1a [KO:K03868] [EC:2.3.2.32]
            100526919  uncharacterized protein LOC100526919 [KO:K03868] [EC:2.3.2.32]
            100798515  RING-box protein 1a [KO:K03868] [EC:2.3.2.32]
            100797895  cullin-4 isoform X1 [KO:K10609]
            100779748  cullin-4 [KO:K10609]
            100805491  cullin-4 [KO:K10609]
            100777459  DNA damage-binding protein 1 [KO:K10610]
            100793506  protein DAMAGED DNA-BINDING 2 isoform X1 [KO:K10140]
            100527914  protein DAMAGED DNA-BINDING 2 [KO:K10140]
            100818100  DNA repair protein RAD4 isoform X1 [KO:K10838]
            100819019  uncharacterized protein LOC100819019 [KO:K10839]
            100818012  ubiquitin receptor RAD23c [KO:K10839]
            100778187  ubiquitin receptor RAD23b isoform X1 [KO:K10839]
            100809066  uncharacterized protein LOC100809066 [KO:K10839]
            100813881  ubiquitin receptor RAD23c-like isoform 1 [KO:K10839]
            100804038  ubiquitin receptor RAD23b [KO:K10839]
            100814162  ubiquitin receptor RAD23c [KO:K10839]
            100817821  ubiquitin receptor RAD23d [KO:K10839]
            100815581  WD repeat-containing protein ATCSA-1 [KO:K10570]
            100790433  WD repeat-containing protein ATCSA-1 [KO:K10570]
            100820025  protein CHROMATIN REMODELING 8 [KO:K10841]
            100814263  cyclin-dependent kinase D-3 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            100786357  cyclin-dependent kinase D-3 isoform X2 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            100776618  LOW QUALITY PROTEIN: cyclin-dependent kinase D-3-like [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            100813673  cyclin-dependent kinase D-3 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            100305654  uncharacterized protein LOC100305654 [KO:K10842]
            547736  cyclin-H1-1 isoform X2 [KO:K06634]
            100800023  cyclin-H1-1 isoform X2 [KO:K06634]
            100790589  cyclin-H1-1 isoform X2 [KO:K06634]
            100818501  general transcription and DNA repair factor IIH helicase subunit XPB1 isoform X2 [KO:K10843] [EC:5.6.2.4]
            100789550  general transcription and DNA repair factor IIH helicase subunit XPB1 isoform X2 [KO:K10843] [EC:5.6.2.4]
            100806384  general transcription and DNA repair factor IIH helicase subunit XPD [KO:K10844] [EC:5.6.2.3]
            100801650  general transcription and DNA repair factor IIH helicase subunit XPD [KO:K10844] [EC:5.6.2.3]
            100795164  general transcription and DNA repair factor IIH subunit TFB5 isoform X2 [KO:K10845]
            100785713  general transcription and DNA repair factor IIH subunit TFB5 [KO:K10845]
            100811780  general transcription and DNA repair factor IIH subunit TFB1-1 isoform X2 [KO:K03141]
            100776016  general transcription and DNA repair factor IIH subunit TFB1-1 [KO:K03141]
            100793016  general transcription factor IIH subunit 2 [KO:K03142]
            100803090  general transcription factor IIH subunit 2 [KO:K03142]
            100776751  uncharacterized protein LOC100776751 [KO:K03143]
            100810574  general transcription and DNA repair factor IIH subunit TFB4 isoform X1 [KO:K03143]
            100784255  general transcription and DNA repair factor IIH subunit TFB2 [KO:K03144]
            100777843  general transcription and DNA repair factor IIH subunit TFB2 isoform X1 [KO:K03144]
            100820295  DNA repair protein UVH3 isoform X1 [KO:K10846]
            100778597  replication protein A 70 kDa DNA-binding subunit A [KO:K07466]
            100792409  replication protein A 70 kDa DNA-binding subunit A [KO:K07466]
            100777091  replication protein A 70 kDa DNA-binding subunit B [KO:K07466]
            100789756  replication protein A 32 kDa subunit A [KO:K10739]
            100782819  replication protein A 32 kDa subunit B [KO:K10739]
            100802512  replication protein A 32 kDa subunit A [KO:K10739]
            100306197  uncharacterized protein LOC100306197 [KO:K10740]
            100306641  uncharacterized protein LOC100306641 [KO:K10740]
            100781484  replication protein A 14 kDa subunit B [KO:K10740]
            100812359  DNA repair endonuclease UVH1 isoform X1 [KO:K10848] [EC:3.1.-.-]
            100777022  DNA excision repair protein ERCC-1 isoform X2 [KO:K10849]
            548092  POLD1; DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
            100817379  DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
            100780072  DNA polymerase delta small subunit [KO:K02328]
            100805951  DNA polymerase delta small subunit isoform X1 [KO:K02328]
            100812372  DNA polymerase delta subunit 3 [KO:K03504]
            100793247  uncharacterized protein LOC100793247 isoform X1 [KO:K03504]
            100778329  DNA polymerase delta subunit 4 [KO:K03505]
            100799459  DNA polymerase delta subunit 4 [KO:K03505]
            100812003  DNA polymerase epsilon catalytic subunit A [KO:K02324] [EC:2.7.7.7]
            100778115  LOW QUALITY PROTEIN: DNA polymerase epsilon catalytic subunit A-like [KO:K02324] [EC:2.7.7.7]
            100784116  DNA polymerase epsilon subunit B isoform X2 [KO:K02325] [EC:2.7.7.7]
            100819488  DNA polymerase epsilon subunit 3 [KO:K02326] [EC:2.7.7.7]
            100306382  uncharacterized protein LOC100306382 [KO:K02326] [EC:2.7.7.7]
            548079  proliferating cell nuclear antigen [KO:K04802]
            100817651  proliferating cell nuclear antigen [KO:K04802]
            100780038  proliferating cell nuclear antigen [KO:K04802]
            100802809  replication factor C subunit 1 [KO:K10754]
            100790070  replication factor C subunit 1 isoform X1 [KO:K10754]
            100788329  replication factor C subunit 2 isoform X1 [KO:K10755]
            100781364  replication factor C subunit 2 [KO:K10755]
            100798331  replication factor C subunit 2 [KO:K10755]
            100775926  replication factor C subunit 2 [KO:K10755]
            100818329  uncharacterized protein LOC100818329 [KO:K10756]
            100782652  replication factor C subunit 3 [KO:K10756]
            100807039  replication factor C subunit 3 isoform X1 [KO:K10756]
            100805231  replication factor C subunit 3 [KO:K10756]
            100817775  uncharacterized protein LOC100817775 isoform X2 [KO:K10756]
            102664389  uncharacterized protein LOC102664389 [KO:K10756]
            100795321  uncharacterized protein LOC100795321 [KO:K10756]
            100783155  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 gmx03020  RNA polymerase
            gmx04120  Ubiquitin mediated proteolysis
KO_PATHWAY  ko03420
///
