ERCC2_ARATH
ID ERCC2_ARATH Reviewed; 758 AA.
AC Q8W4M7; Q9SE44; Q9ZVS1;
DT 04-JAN-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPD;
DE Short=TFIIH subunit XPD;
DE EC=3.6.4.12;
DE AltName: Full=ERCC2 homolog;
DE AltName: Full=RAD3 homolog;
DE AltName: Full=UV hypersensitive protein 6;
DE Short=AtUVH6;
DE AltName: Full=XPD homolog;
DE Short=AtXPD {ECO:0000303|PubMed:15645454};
GN Name=XPD {ECO:0000303|PubMed:16623910}; Synonyms=UVH6;
GN OrderedLocusNames=At1g03190; ORFNames=F15K9.20;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, AND MUTAGENESIS
RP OF GLY-521.
RC STRAIN=cv. Columbia;
RX PubMed=12857822; DOI=10.1104/pp.103.021808;
RA Liu Z., Hong S.-W., Escobar M., Vierling E., Mitchell D.L., Mount D.W.,
RA Hall J.D.;
RT "Arabidopsis UVH6, a homolog of human XPD and yeast RAD3 DNA repair genes,
RT functions in DNA repair and is essential for plant growth.";
RL Plant Physiol. 132:1405-1414(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Vonarx E.J., Kunz B.A.;
RT "A Rad3/XP-D/ERCC2 homolog from Arabidopsis thaliana.";
RL Submitted (SEP-1999) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP MUTANT UVH6-1.
RX PubMed=7498749; DOI=10.1093/genetics/140.2.725;
RA Jenkins M.E., Harlow G.R., Liu Z., Shotwell M.A., Ma J., Mount D.W.;
RT "Radiation-sensitive mutants of Arabidopsis thaliana.";
RL Genetics 140:725-732(1995).
RN [7]
RP FUNCTION.
RX PubMed=9414549; DOI=10.1104/pp.115.4.1351;
RA Jenkins M.E., Suzuki T.C., Mount D.W.;
RT "Evidence that heat and ultraviolet radiation activate a common stress-
RT response program in plants that is altered in the uvh6 mutant of
RT Arabidopsis thaliana.";
RL Plant Physiol. 115:1351-1358(1997).
RN [8]
RP COMPONENT OF TFIIH CORE COMPLEX, AND NOMENCLATURE.
RX PubMed=15645454; DOI=10.1002/em.20094;
RA Kunz B.A., Anderson H.J., Osmond M.J., Vonarx E.J.;
RT "Components of nucleotide excision repair and DNA damage tolerance in
RT Arabidopsis thaliana.";
RL Environ. Mol. Mutagen. 45:115-127(2005).
RN [9]
RP INTERACTION WITH GTF2H2.
RX PubMed=16623910; DOI=10.1111/j.1365-313x.2006.02705.x;
RA Vonarx E.J., Tabone E.K., Osmond M.J., Anderson H.J., Kunz B.A.;
RT "Arabidopsis homologue of human transcription factor IIH/nucleotide
RT excision repair factor p44 can function in transcription and DNA repair and
RT interacts with AtXPD.";
RL Plant J. 46:512-521(2006).
RN [10]
RP GENE FAMILY.
RX PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA Xu R., Zhang S., Huang J., Zheng C.;
RT "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT sativa.";
RL PLoS ONE 8:E78982-E78982(2013).
CC -!- FUNCTION: ATP-dependent 5'-3' DNA helicase, component of the general
CC transcription and DNA repair factor IIH (TFIIH) core complex, which is
CC involved in general and transcription-coupled nucleotide excision
CC repair (NER) of damaged DNA and, when complexed to CAK, in RNA
CC transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA
CC around the lesion to allow the excision of the damaged oligonucleotide
CC and its replacement by a new DNA fragment. The ATP-dependent helicase
CC activity of XPD is required for DNA opening. In transcription, TFIIH
CC has an essential role in transcription initiation. When the pre-
CC initiation complex (PIC) has been established, TFIIH is required for
CC promoter opening and promoter escape. Phosphorylation of the C-terminal
CC tail (CTD) of the largest subunit of RNA polymerase II by the kinase
CC module CAK controls the initiation of transcription. XPD acts by
CC forming a bridge between CAK and the core-TFIIH complex (By
CC similarity). Essential during plant growth (PubMed:12857822). May
CC negatively regulate a common response program mediated by UV damage and
CC heat stress, that leads to tissue death and reduced chloroplast
CC function (PubMed:9414549). {ECO:0000250|UniProtKB:P18074,
CC ECO:0000269|PubMed:12857822, ECO:0000269|PubMed:9414549}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000250};
CC -!- SUBUNIT: Component of the 7-subunit TFIIH core complex composed of XPB,
CC XPD, TFB1/GTF2H1, GTF2H2/P44, TFB4/GTF2H3, TFB2/GTF2H4 and TFB5/GTF2H5,
CC which is active in NER. The core complex associates with the 3-subunit
CC CDK-activating kinase (CAK) module composed of CYCH1/cyclin H1, CDKD
CC and MAT1/At4g30820 to form the 10-subunit holoenzyme (holo-TFIIH)
CC active in transcription (By similarity). Interacts with GTF2H2/P44
CC (PubMed:16623910). {ECO:0000250|UniProtKB:P18074,
CC ECO:0000269|PubMed:16623910, ECO:0000305|PubMed:15645454}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed at low levels in all tissues.
CC {ECO:0000269|PubMed:12857822}.
CC -!- SIMILARITY: Belongs to the helicase family. RAD3/XPD subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC72116.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AY090788; AAM10793.1; -; mRNA.
DR EMBL; AF188623; AAF14582.1; -; mRNA.
DR EMBL; AC005278; AAC72116.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE27542.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27543.1; -; Genomic_DNA.
DR EMBL; AY062471; AAL32549.1; -; mRNA.
DR EMBL; AY090915; AAM13910.1; -; mRNA.
DR EMBL; BT010344; AAQ56787.1; -; mRNA.
DR PIR; C86163; C86163.
DR RefSeq; NP_171818.1; NM_100201.3.
DR RefSeq; NP_849584.1; NM_179253.1.
DR AlphaFoldDB; Q8W4M7; -.
DR SMR; Q8W4M7; -.
DR BioGRID; 24792; 11.
DR IntAct; Q8W4M7; 10.
DR STRING; 3702.AT1G03190.2; -.
DR iPTMnet; Q8W4M7; -.
DR PaxDb; Q8W4M7; -.
DR PRIDE; Q8W4M7; -.
DR ProteomicsDB; 220670; -.
DR EnsemblPlants; AT1G03190.1; AT1G03190.1; AT1G03190.
DR EnsemblPlants; AT1G03190.2; AT1G03190.2; AT1G03190.
DR GeneID; 839557; -.
DR Gramene; AT1G03190.1; AT1G03190.1; AT1G03190.
DR Gramene; AT1G03190.2; AT1G03190.2; AT1G03190.
DR KEGG; ath:AT1G03190; -.
DR Araport; AT1G03190; -.
DR TAIR; locus:2014525; AT1G03190.
DR eggNOG; KOG1131; Eukaryota.
DR HOGENOM; CLU_011312_1_0_1; -.
DR InParanoid; Q8W4M7; -.
DR OMA; IREQFFR; -.
DR OrthoDB; 186062at2759; -.
DR PhylomeDB; Q8W4M7; -.
DR PRO; PR:Q8W4M7; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8W4M7; baseline and differential.
DR Genevisible; Q8W4M7; AT.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003684; F:damaged DNA binding; IBA:GO_Central.
DR GO; GO:0003678; F:DNA helicase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IMP:TAIR.
DR GO; GO:0000717; P:nucleotide-excision repair, DNA duplex unwinding; IBA:GO_Central.
DR GO; GO:0033683; P:nucleotide-excision repair, DNA incision; IBA:GO_Central.
DR GO; GO:0045951; P:positive regulation of mitotic recombination; IBA:GO_Central.
DR GO; GO:0009408; P:response to heat; IMP:TAIR.
DR GO; GO:0009411; P:response to UV; IMP:TAIR.
DR GO; GO:0006366; P:transcription by RNA polymerase II; IBA:GO_Central.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR006555; ATP-dep_Helicase_C.
DR InterPro; IPR010614; DEAD_2.
DR InterPro; IPR045028; DinG/Rad3-like.
DR InterPro; IPR002464; DNA/RNA_helicase_DEAH_CS.
DR InterPro; IPR010643; HBB.
DR InterPro; IPR014013; Helic_SF1/SF2_ATP-bd_DinG/Rad3.
DR InterPro; IPR006554; Helicase-like_DEXD_c2.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR013020; Rad3/Chl1-like.
DR InterPro; IPR001945; RAD3/XPD.
DR PANTHER; PTHR11472; PTHR11472; 1.
DR PANTHER; PTHR11472:SF1; PTHR11472:SF1; 1.
DR Pfam; PF06733; DEAD_2; 1.
DR Pfam; PF06777; HBB; 1.
DR Pfam; PF13307; Helicase_C_2; 1.
DR PRINTS; PR00852; XRODRMPGMNTD.
DR SMART; SM00488; DEXDc2; 1.
DR SMART; SM00491; HELICc2; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00604; rad3; 1.
DR PROSITE; PS00690; DEAH_ATP_HELICASE; 1.
DR PROSITE; PS51193; HELICASE_ATP_BIND_2; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; ATP-binding; DNA damage; DNA repair; DNA-binding; Helicase;
KW Hydrolase; Iron; Iron-sulfur; Metal-binding; Nucleotide-binding; Nucleus;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..758
FT /note="General transcription and DNA repair factor IIH
FT helicase subunit XPD"
FT /id="PRO_0000101982"
FT DOMAIN 7..285
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOTIF 234..238
FT /note="DEAH box"
FT BINDING 42..49
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 116
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 134
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 155
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 190
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT MUTAGEN 521
FT /note="G->E: In uvh6-1; confers increased sensitivity to UV
FT light and heat, yellow-green leaf coloration, and mild
FT growth defects."
FT /evidence="ECO:0000269|PubMed:12857822"
FT CONFLICT 559
FT /note="K -> E (in Ref. 2; AAF14582)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 758 AA; 86236 MW; C5659DBE6219B1A6 CRC64;
MIFKIEDVTV YFPYDNIYPE QYEYMVELKR ALDAKGHCLL EMPTGTGKTI ALLSLITSYR
LSRPDSPIKL VYCTRTVHEM EKTLGELKLL HDYQVRHLGT QAKILALGLS SRKNLCVNTK
VLAAENRDSV DAACRKRTAS WVRALSTENP NVELCDFFEN YEKAAENALL PPGVYTLEDL
RAFGKNRGWC PYFLARHMIQ FANVIVYSYQ YLLDPKVAGF ISKELQKESV VVFDEAHNID
NVCIEALSVS VRRVTLEGAN RNLNKIRQEI DRFKATDAGR LRAEYNRLVE GLALRGDLSG
GDQWLANPAL PHDILKEAVP GNIRRAEHFV HVLRRLLQYL GVRLDTENVE KESPVSFVSS
LNSQAGIEQK TLKFCYDRLQ SLMLTLEITD TDEFLPIQTV CDFATLVGTY ARGFSIIIEP
YDERMPHIPD PILQLSCHDA SLAIKPVFDR FQSVVITSGT LSPIDLYPRL LNFTPVVSRS
FKMSMTRDCI CPMVLTRGSD QLPVSTKFDM RSDPGVVRNY GKLLVEMVSI VPDGVVCFFV
SYSYMDGIIA TWNETGILKE IMQQKLVFIE TQDVVETTLA LDNYRRACDC GRGAVFFSVA
RGKVAEGIDF DRHYGRLVVM YGVPFQYTLS KILRARLEYL HDTFQIKEGD FLTFDALRQA
AQCVGRVIRS KADYGMMIFA DKRYSRHDKR SKLPGWILSH LRDAHLNLST DMAIHIAREF
LRKMAQPYDK AGTMGRKTLL TQEDLEKMAE TGVQDMAY
