ENTRY       mtr03420                    Pathway
NAME        Nucleotide excision repair - Medicago truncatula (barrel medic)
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 mtr03420  Nucleotide excision repair
DBLINKS     GO: 0006289
ORGANISM    Medicago truncatula (barrel medic) [GN:mtr]
GENE        11444798  DNA polymerase I A, chloroplastic/mitochondrial isoform X1 [KO:K02335] [EC:2.7.7.7]
            11436067  DNA polymerase I A, chloroplastic/mitochondrial [KO:K02335] [EC:2.7.7.7]
            11444264  DNA polymerase I A, chloroplastic/mitochondrial isoform X2 [KO:K02335] [EC:2.7.7.7]
            11413962  RING-box protein 1a [KO:K03868] [EC:2.3.2.32]
            25492127  RING-box protein 1a [KO:K03868] [EC:2.3.2.32]
            11437813  cullin-4 [KO:K10609]
            11435521  DNA damage-binding protein 1 [KO:K10610]
            11405495  protein DAMAGED DNA-BINDING 2 [KO:K10140]
            11436447  DNA repair protein RAD4 isoform X1 [KO:K10838]
            25499820  ubiquitin receptor RAD23d [KO:K10839]
            25488002  ubiquitin receptor RAD23b [KO:K10839]
            25485511  ubiquitin receptor RAD23c [KO:K10839]
            25489968  WD repeat-containing protein ATCSA-1 isoform X2 [KO:K10570]
            25484243  protein CHROMATIN REMODELING 8 [KO:K10841]
            25496775  cyclin-dependent kinase D-3 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            25489030  cyclin-dependent kinase D-3 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            11434892  CDK-activating kinase assembly factor MAT1 isoform X1 [KO:K10842]
            11415666  cyclin-H1-1 [KO:K06634]
            25502076  general transcription and DNA repair factor IIH helicase subunit XPB1 [KO:K10843] [EC:5.6.2.4]
            25487506  general transcription and DNA repair factor IIH helicase subunit XPD [KO:K10844] [EC:5.6.2.3]
            11411289  general transcription and DNA repair factor IIH subunit TFB5 [KO:K10845]
            11406059  general transcription and DNA repair factor IIH subunit TFB5 [KO:K10845]
            25496637  general transcription and DNA repair factor IIH subunit TFB1-1 [KO:K03141]
            11406928  general transcription and DNA repair factor IIH subunit TFB1-1 [KO:K03141]
            11417626  general transcription factor IIH subunit 2 [KO:K03142]
            11419054  general transcription and DNA repair factor IIH subunit TFB4 isoform X1 [KO:K03143]
            11406173  general transcription and DNA repair factor IIH subunit TFB2 isoform X1 [KO:K03144]
            25493180  general transcription and DNA repair factor IIH subunit TFB2 [KO:K03144]
            25498004  DNA repair protein UVH3 isoform X1 [KO:K10846]
            25493890  replication protein A 70 kDa DNA-binding subunit B [KO:K07466]
            25486480  replication protein A 70 kDa DNA-binding subunit A [KO:K07466]
            11446020  replication protein A 32 kDa subunit B [KO:K10739]
            25481878  replication protein A 32 kDa subunit A [KO:K10739]
            11433064  replication protein A 14 kDa subunit B [KO:K10740]
            25485573  replication protein A 14 kDa subunit B [KO:K10740]
            25485575  replication protein A 14 kDa subunit B [KO:K10740]
            11442992  DNA repair endonuclease UVH1 [KO:K10848] [EC:3.1.-.-]
            11412075  DNA excision repair protein ERCC-1 [KO:K10849]
            25489857  DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
            11437014  DNA polymerase delta small subunit [KO:K02328]
            11408397  DNA polymerase delta subunit 3 isoform X1 [KO:K03504]
            25493347  DNA polymerase delta subunit 4 [KO:K03505]
            25493349  DNA polymerase delta subunit 4 [KO:K03505]
            25485289  DNA polymerase delta subunit 4 [KO:K03505]
            11445193  DNA polymerase epsilon catalytic subunit A isoform X1 [KO:K02324] [EC:2.7.7.7]
            25496685  DNA polymerase epsilon subunit B [KO:K02325] [EC:2.7.7.7]
            25492285  DNA polymerase epsilon subunit 3 [KO:K02326] [EC:2.7.7.7]
            25490757  proliferating cell nuclear antigen [KO:K04802]
            25492173  replication factor C subunit 1 isoform X1 [KO:K10754]
            11414806  replication factor C subunit 2 [KO:K10755]
            25493662  replication factor C subunit 2 [KO:K10755]
            11414029  replication factor C subunit 3 [KO:K10756]
            11429308  uncharacterized protein LOC11429308 [KO:K10756]
            25495823  replication factor C subunit 3 [KO:K10756]
            25497284  replication factor C subunit 3 [KO:K10756]
            120575764  uncharacterized protein LOC120575764 [KO:K10756]
            25492370  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 mtr03020  RNA polymerase
            mtr04120  Ubiquitin mediated proteolysis
KO_PATHWAY  ko03420
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