nucleotide excision repair (NER)

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DESCRIPTION:

Nucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage and photoproducts 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.

EXTERNAL DATABASES:
KEGG database - NER - Homo sapiens (human) 
KEGG database - NER - Mus musculus (mouse)
KEGG database - NER - Caenorhabditis elegans (nematode)
KEGG database - NER - Drosophila melanogaster (fruit fly)
KEGG database - NER - Saccharomyces cerevisiae (budding yeast) 
KEGG database - NER - DNA replication - Schizosaccharomyces pombe (fission yeast)
KEGG database - NER - Escherichia coli K-12 MG1655
KEGG database - NER - Arabidopsis thaliana (thale cress)


ABBREVIATIONS:
NER


RELATED DISEASES:

XFE progeroid syndrome (XFEPS)
TrichoThioDystrophy Photosensitive (TTDP)
cerebro-oculo-facio-skeletal syndrome 3 (COFS3)
xeroderma pigmentosum, complementation group A (XPA)
xeroderma pigmentosum, complementation group D (XPD)
cerebro-oculo-facio-skeletal syndrome 4 (COFS4)
Cockayne syndrome, TYPE A
Cockayne syndrome, TYPE B (CSB)
xeroderma pigmentosum, complementation group F (XPF)
xeroderma pigmentosum, complementation group C (XPC)
cerebro-oculo-facio-skeletal syndrome type 1 (COFS1)
xeroderma pigmentosum, complementation group G (XPG)
age-related macular degeneration type 5 (ARMD5)
UV-sensitive syndrome (UVS)
xeroderma pigmentosum, complementation group E (XPE)
De Sanctis-Cacchione syndrome (DSC)
xeroderma pigmentosum, complementation group B (XPB)
cerebro-oculo-facio-skeletal syndrome type 2 (COFS2)
lung cancer

DAMAGES RECOGNIZED AND REMOVED:


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ORTHOLOGY CLASS Homo sapiens L. (human) [HSA] Mus musculus L. (mouse) [MMU] Caenorhabditis elegans Maupas (nematode) [CEL] Drosophila melanogaster Meigen (fruit fly) [DME] Saccharomyces cerevisiae Meyen ex E.C. Hansen (budding yeast) [SCE] Schizo-saccharomyces pombe Lindner (fission yeast) [SPO] Escherichia coli Migula (bacterium) K-12 MG1655 [ECO] Arabidopsis thaliana (L.) Heynh. (mouse-ear cress) [ATH]
ko:K10849 (DNA excision repair protein ERCC-1) ERCC1 Ercc1 gi:25144926 Ercc1 RAD10 swi10 ERCC1
ko:K10848 (DNA excision repair protein ERCC-4 [EC:3.1.-.-]) ERCC4 (XPF) Ercc4 C47D12.8 mei-9 RAD1 rad16 UVH1
ko:K10847 (DNA-repair protein complementing XP-A cells) XPA Xpa xpa-1 Xpac RAD14 rhp14
ko:K10846 (DNA excision repair protein ERCC-5) ERCC5 (XPG) Ercc5 xpg-1 mus201 RAD2 rad13 UVH3
ko:K10845 (TFIIH basal transcription factor complex TTD-A subunit) GTF2H5 Gtf2h5 gi:17556222 Tfb5 TFB5 tfb5 gi:15221323
gi:15221323
ko:K10844 (DNA excision repair protein ERCC-2 [EC:3.6.4.12]) ERCC2 (XPD) Ercc2 gi:71994598 Xpd RAD3 rad15 UVH6
UVH6
ko:K10843 (DNA excision repair protein ERCC-3 [EC:3.6.4.12]) ERCC3 (XPB) Ercc3 gi:17556358 hay SSL2 ptr8 XPB2
XPB2
ko:K10842 (CDK-activating kinase assembly factor MAT1) MNAT1 Mnat1 mnat-1 Mat1 TFB3 pmh1 gi:145334183
gi:145334183
ko:K10841 (DNA excision repair protein ERCC-6) ERCC6 (CSB) Ercc6 csb-1 RAD26 rhp26 CHR8
ko:K10840 (centrin-2) CETN2 Cetn2
ko:K10839 (UV excision repair protein RAD23) RAD23B
RAD23A
Rad23a
Rad23b
rad-23 Rad23 RAD23 rhp23 gi:15221013
RAD23
gi:15232924
gi:145334669
ko:K10838 (xeroderma pigmentosum group C-complementing protein) XPC Xpc xpc-1 mus210 RAD4
RAD4
rhp42
rhp41
RAD4
ko:K10756 (replication factor C subunit 3/5) RFC3
RFC5
Rfc5
Rfc3
rfc-3
ARPA
RfC3
RfC38
RFC3
RFC5
rfc3
rfc5
RFC3
putative RFC3/5
ko:K10755 (replication factor C subunit 2/4) RFC2
RFC4
Rfc4
Rfc2
rfc-4
rfc-2
RfC4
CG8142
RFC2
RFC4
rfc2
rfc4
RFC2/4
RFC2
ko:K10754 (replication factor C subunit 1) RFC1 Rfc1 rfc-1 Gnf1 RFC1 rfc1 AtRFC1
ko:K10747 (DNA ligase 1 [EC:6.5.1.1]) LIG1 Lig1 lig-1 DmDNA Lig I CDC9 adl1
cdc17
At1g49250
ATLIG1
ko:K10741 (replication factor A4) RPA4
ko:K10740 (replication factor A3) RPA3 Rpa3 Dmel_CG15220 ssb3 At4g18590
F3C22_30
ko:K10739 (replication factor A2) RPA2 Rpa2 rpa-2
rpa-4
RPA2 RFA2 ssb2 RPA2
RPA32B
ko:K10610 (DNA damage-binding protein 1) DDB1 Ddb1 ddb-1 pic ddb1 DDB1A
DDB1B
ko:K10609 (cullin 4) CUL4B
CUL4A
Cul4b
Cul4a
cul-4 cul-4 pcu4 CUL4
ko:K10570 (DNA excision repair protein ERCC-8) ERCC8 (CSA) Ercc8 RAD28 gi:19112099 ATCSA-1
gi:22329677
ko:K10140 (DNA damage-binding protein 2) DDB2 (XPE) Ddb2 DDB2
ko:K07466 (replication factor A1) RPA1 Rpa1 rpa-1 RpA-70 RFA1 ssb1 RPA1A
ko:K06634 (cyclin H) CCNH Ccnh cyh-1 CycH CCL1 mcs2 CYCH;1
CYCH;1
ko:K04802 (proliferating cell nuclear antigen) PCNA Pcna pcn-1 Mus209 (Pcna)
Pcna2
POL30 pcn1 PCNA1
PCNA2
ko:K03868 (RING-box protein 1) RBX1 Rbx1 rbx-1 Roc1b
Roc1a
HRT1 rbx1 gi:15229164
RBX1
ko:K03723 (transcription-repair coupling factor (superfamily II helicase) [EC:3.6.4.-]) Mfd
ko:K03703 (excinuclease ABC subunit C) UvrC
ko:K03702 (excinuclease ABC subunit B) UvrB
ko:K03701 (excinuclease ABC subunit A) UvrA
ko:K03657 (DNA helicase II / ATP-dependent DNA helicase PcrA [EC:3.6.4.12]) SRS2 srs2 UvrD
ko:K03506 (DNA polymerase epsilon subunit 4 [EC:2.7.7.7]) POLE4 Pole4 DNA Pol epsilon sub 4 Mes4 DPB3 SPCC16C4.22
ko:K03505 (DNA polymerase delta subunit 4) POLD4 Pold4 cdm1 POLD4
ko:K03504 (DNA polymerase delta subunit 3) POLD3 Pold3 PolD3 CG3975
Dmel_CG3975
POL32 cdc27 POLD3
ko:K03144 (transcription initiation factor TFIIH subunit 4) GTF2H4 Gtf2h4 gi:32565796 mrn TFB2 tfb2 gi:334186626
gi:42566894
ko:K03143 (transcription initiation factor TFIIH subunit 3) GTF2H3 Gtf2h3 TFIIH sub 3 (hypothetical protein) Tfb4 TFB4 tfb4 gi:18394597
gi:18394597
ko:K03142 (transcription initiation factor TFIIH subunit 2) GTF2H2
GTF2H2C
GTF2H2D
Gtf2h2 gi:17555086 Ssl1 SSL1 ssl1 GTF2H2
GTF2H2
ko:K03141 (transcription initiation factor TFIIH subunit 1) GTF2H1 Gtf2h1 gi:71992201 Tfb1 TFB1 tfb1 gi:42562765
gi:240255685
gi:240255685
gi:42562765
ko:K02335 (DNA polymerase I [EC:2.7.7.7]) DNA Pol I POLGAMMA2
POLGAMMA1
ko:K02328 (DNA polymerase delta subunit 2) POLD2 Pold2 DNA Pol delta sub 2 DNA pol delta small sub POL31 cdc1 POLD2
ko:K02327 (DNA polymerase delta subunit 1 [EC:2.7.7.7]) POLδ (POLD) mPolδ (mPolD) DNA Pol delta DNApol-delta POL3
POL3
cdc6 POLD1
ko:K02326 (DNA polymerase epsilon subunit 3 [EC:2.7.7.7]) POLE3 Pole3 Chrac-14 DPB4 dpb4
ko:K02325 (DNA polymerase epsilon subunit 2 [EC:2.7.7.7]) POLE2 Pole2 DNA Pole-2 Pole2 DPB2 dpb2 ATDPB2
ko:K02324 (DNA polymerase epsilon subunit 1 [EC:2.7.7.7]) POLε (POLE) mPolε (mPolE) DNA Pol epsilon sub 1 (hypothetical protein) DNApol-epsilon POL2 cdc20 TIL1
TIL2
ko:K02202 (cyclin-dependent kinase 7 [EC:2.7.11.22]) CDK7 Cdk7 cdk-7 Cdk7 KIN28 mcs6 gi:15220917
CAK4
gi:15219522
CAK4
CDKD1;3
CDKD1;1
ko:K01972 (DNA ligase (NAD+) [EC:6.5.1.2]) DNA ligase I
DNA ligase B

Last modification date: Oct. 11, 2011