ENTRY       ath03420                    Pathway
NAME        Nucleotide excision repair - Arabidopsis thaliana (thale cress)
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 ath03420  Nucleotide excision repair
DBLINKS     GO: 0006289
ORGANISM    Arabidopsis thaliana (thale cress) [GN:ath]
GENE        AT1G50840  POLGAMMA2; polymerase gamma 2 [KO:K02335] [EC:2.7.7.7]
            AT3G20540  POLGAMMA1; polymerase gamma 1 [KO:K02335] [EC:2.7.7.7]
            AT3G42830  RING/U-box superfamily protein [KO:K03868] [EC:2.3.2.32]
            AT5G20570  RBX1; RING-box 1 [KO:K03868] [EC:2.3.2.32]
            AT5G46210  CUL4; cullin4 [KO:K10609]
            AT3G46910  Cullin family protein [KO:K10609]
            AT4G12100  Cullin family protein [KO:K10609]
            AT4G05420  DDB1A; damaged DNA binding protein 1A [KO:K10610]
            AT4G21100  DDB1B; damaged DNA binding protein 1B [KO:K10610]
            AT5G58760  DDB2; damaged DNA binding 2 [KO:K10140]
            AT5G16630  RAD4; DNA repair protein Rad4 family [KO:K10838]
            AT1G16190  RAD23A; Rad23 UV excision repair protein family [KO:K10839]
            AT1G79650  RAD23B; Rad23 UV excision repair protein family [KO:K10839]
            AT5G38470  RAD23D; Rad23 UV excision repair protein family [KO:K10839]
            AT3G02540  RAD23C; Rad23 UV excision repair protein family [KO:K10839]
            AT5G16090  RAD23 UV excision repair family protein [KO:K10839]
            AT1G19750  Transducin/WD40 repeat-like superfamily protein [KO:K10570]
            AT1G27840  ATCSA-1; Transducin/WD40 repeat-like superfamily protein [KO:K10570]
            AT2G18760  CHR8; chromatin remodeling 8 [KO:K10841]
            AT1G18040  CDKD1;3; cyclin-dependent kinase D1;3 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            AT1G66750  CAK4; CDK-activating kinase 4 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            AT1G73690  CDKD1;1; cyclin-dependent kinase D1;1 [KO:K02202] [EC:2.7.11.22 2.7.11.23]
            AT4G30820  cyclin-dependent kinase-activating kinase assembly factor-related / CDK-activating kinase assembly factor-like protein [KO:K10842]
            AT5G27620  CYCH;1; cyclin H;1 [KO:K06634]
            AT5G41360  XPB2; homolog of Xeroderma pigmentosum complementation group B 2 [KO:K10843] [EC:5.6.2.4]
            AT5G41370  XPB1; DNA repair helicase XPB1-like protein [KO:K10843] [EC:5.6.2.4]
            AT1G03190  UVH6; RAD3-like DNA-binding helicase protein [KO:K10844] [EC:5.6.2.3]
            AT1G12400  Nucleotide excision repair, TFIIH, subunit TTDA [KO:K10845]
            AT1G62886  Nucleotide excision repair, TFIIH, subunit TTDA [KO:K10845]
            AT3G61420  BSD domain (BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins) [KO:K03141]
            AT1G55750  BSD domain (BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins) [KO:K03141]
            AT1G05055  GTF2H2; general transcription factor II H2 [KO:K03142]
            AT1G18340  basal transcription factor complex subunit-like protein [KO:K03143]
            AT4G17020  transcription factor-like protein [KO:K03144]
            AT3G28030  UVH3; 5'-3' exonuclease family protein [KO:K10846]
            AT5G45400  RPA70C; Replication factor-A protein 1-like protein [KO:K07466]
            AT4G19130  Replication factor-A protein 1-like protein [KO:K07466]
            AT2G06510  RPA1A; replication protein A 1A [KO:K07466]
            AT5G61000  RPA70D; Replication factor-A protein 1-like protein [KO:K07466]
            AT5G08020  RPA70B; RPA70-kDa subunit B [KO:K07466]
            AT2G24490  RPA2; replicon protein A2 [KO:K10739]
            AT3G02920  RPA32B; Replication protein A, subunit RPA32 [KO:K10739]
            AT3G52630  Nucleic acid-binding, OB-fold-like protein [KO:K10740]
            AT4G18590  Nucleic acid-binding, OB-fold-like protein [KO:K10740]
            AT5G41150  UVH1; Restriction endonuclease, type II-like superfamily protein [KO:K10848] [EC:3.1.-.-]
            AT3G05210  ERCC1; nucleotide repair protein [KO:K10849]
            AT5G63960  DNA polymerase delta subunit 1 [KO:K02327] [EC:2.7.7.7]
            AT2G42120  POLD2; DNA polymerase delta small subunit [KO:K02328]
            AT1G78650  POLD3; DNA-directed DNA polymerase [KO:K03504]
            AT1G09815  POLD4; polymerase delta 4 [KO:K03505]
            AT1G08260  TIL1; DNA polymerase epsilon catalytic subunit [KO:K02324] [EC:2.7.7.7]
            AT2G27120  TIL2; DNA polymerase epsilon catalytic subunit [KO:K02324] [EC:2.7.7.7]
            AT5G22110  DPB2; DNA polymerase epsilon subunit B2 [KO:K02325] [EC:2.7.7.7]
            AT2G27470  NF-YB11; nuclear factor Y, subunit B11 [KO:K02326] [EC:2.7.7.7]
            AT2G29570  PCNA2; proliferating cell nuclear antigen 2 [KO:K04802]
            AT1G07370  PCNA1; proliferating cellular nuclear antigen 1 [KO:K04802]
            AT5G22010  RFC1; replication factor C1 [KO:K10754]
            AT1G21690  EMB1968; ATPase family associated with various cellular activities (AAA) [KO:K10755]
            AT1G63160  RFC2; replication factor C 2 [KO:K10755]
            AT1G77470  RFC3; replication factor C subunit 3 [KO:K10756]
            AT5G27740  EMB2775; ATPase family associated with various cellular activities (AAA) [KO:K10756]
            AT1G08130  LIG1; 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 ath03020  RNA polymerase
            ath04120  Ubiquitin mediated proteolysis
KO_PATHWAY  ko03420
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