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DNA repair helicase XPD (EC 3.6.4.12) (ERCC2 homolog) (RAD3 homolog) (UV hypersensitive protein 6) (AtUVH6) (XPD homolog) (AtXPD)

 ERCC2_ARATH             Reviewed;         758 AA.
Q8W4M7; Q9SE44; Q9ZVS1;
04-JAN-2005, integrated into UniProtKB/Swiss-Prot.
01-MAR-2002, sequence version 1.
22-NOV-2017, entry version 118.
RecName: Full=DNA repair helicase XPD;
EC=3.6.4.12;
AltName: Full=ERCC2 homolog;
AltName: Full=RAD3 homolog;
AltName: Full=UV hypersensitive protein 6;
Short=AtUVH6;
AltName: Full=XPD homolog;
Short=AtXPD {ECO:0000303|PubMed:15645454};
Name=XPD {ECO:0000303|PubMed:16623910}; Synonyms=UVH6;
OrderedLocusNames=At1g03190; ORFNames=F15K9.20;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, AND
MUTAGENESIS OF GLY-521.
STRAIN=cv. Columbia;
PubMed=12857822; DOI=10.1104/pp.103.021808;
Liu Z., Hong S.-W., Escobar M., Vierling E., Mitchell D.L.,
Mount D.W., Hall J.D.;
"Arabidopsis UVH6, a homolog of human XPD and yeast RAD3 DNA repair
genes, functions in DNA repair and is essential for plant growth.";
Plant Physiol. 132:1405-1414(2003).
[2]
NUCLEOTIDE SEQUENCE [MRNA].
Vonarx E.J., Kunz B.A.;
"A Rad3/XP-D/ERCC2 homolog from Arabidopsis thaliana.";
Submitted (SEP-1999) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130712; DOI=10.1038/35048500;
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S.,
White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M.,
Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
"Sequence and analysis of chromosome 1 of the plant Arabidopsis
thaliana.";
Nature 408:816-820(2000).
[4]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[6]
MUTANT UVH6-1.
PubMed=7498749;
Jenkins M.E., Harlow G.R., Liu Z., Shotwell M.A., Ma J., Mount D.W.;
"Radiation-sensitive mutants of Arabidopsis thaliana.";
Genetics 140:725-732(1995).
[7]
FUNCTION.
PubMed=9414549; DOI=10.1104/pp.115.4.1351;
Jenkins M.E., Suzuki T.C., Mount D.W.;
"Evidence that heat and ultraviolet radiation activate a common
stress-response program in plants that is altered in the uvh6 mutant
of Arabidopsis thaliana.";
Plant Physiol. 115:1351-1358(1997).
[8]
COMPONENT OF TFIIH CORE COMPLEX, AND NOMENCLATURE.
PubMed=15645454; DOI=10.1002/em.20094;
Kunz B.A., Anderson H.J., Osmond M.J., Vonarx E.J.;
"Components of nucleotide excision repair and DNA damage tolerance in
Arabidopsis thaliana.";
Environ. Mol. Mutagen. 45:115-127(2005).
[9]
INTERACTION WITH GTF2H2.
PubMed=16623910; DOI=10.1111/j.1365-313X.2006.02705.x;
Vonarx E.J., Tabone E.K., Osmond M.J., Anderson H.J., Kunz B.A.;
"Arabidopsis homologue of human transcription factor IIH/nucleotide
excision repair factor p44 can function in transcription and DNA
repair and interacts with AtXPD.";
Plant J. 46:512-521(2006).
[10]
GENE FAMILY.
PubMed=24265739; DOI=10.1371/journal.pone.0078982;
Xu R., Zhang S., Huang J., Zheng C.;
"Genome-wide comparative in silico analysis of the RNA helicase gene
family in Zea mays and Glycine max: a comparison with Arabidopsis and
Oryza sativa.";
PLoS ONE 8:E78982-E78982(2013).
-!- FUNCTION: Putative ATP-dependent 5'-3' DNA helicase involved in
nucleotide excision repair (NER) of UV-damaged DNA. May open DNA
around the damage. Essential during plant growth. May negatively
regulate a common response program mediated by UV damage and heat
stress, that leads to tissue death and reduced chloroplast
function. {ECO:0000269|PubMed:12857822,
ECO:0000269|PubMed:9414549}.
-!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000250};
Note=Binds 1 [4Fe-4S] cluster. {ECO:0000250};
-!- SUBUNIT: Component of the TFIIH core complex, which is composed of
7 subunits, XPD, XPB, TFB1/GTF2H1, GTF2H2/P44, TFB4/GTF2H3,
TFB2/GTF2H4 and TFB5/GTF2H5 (Probable). Interacts with GTF2H2/P44
(PubMed:16623910). {ECO:0000269|PubMed:16623910,
ECO:0000305|PubMed:15645454}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
-!- TISSUE SPECIFICITY: Expressed at low levels in all tissues.
{ECO:0000269|PubMed:12857822}.
-!- SIMILARITY: Belongs to the helicase family. RAD3/XPD subfamily.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAC72116.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AY090788; AAM10793.1; -; mRNA.
EMBL; AF188623; AAF14582.1; -; mRNA.
EMBL; AC005278; AAC72116.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002684; AEE27542.1; -; Genomic_DNA.
EMBL; CP002684; AEE27543.1; -; Genomic_DNA.
EMBL; AY062471; AAL32549.1; -; mRNA.
EMBL; AY090915; AAM13910.1; -; mRNA.
EMBL; BT010344; AAQ56787.1; -; mRNA.
PIR; C86163; C86163.
RefSeq; NP_171818.1; NM_100201.3.
RefSeq; NP_849584.1; NM_179253.1.
UniGene; At.10863; -.
ProteinModelPortal; Q8W4M7; -.
BioGrid; 24792; 11.
IntAct; Q8W4M7; 10.
STRING; 3702.AT1G03190.1; -.
iPTMnet; Q8W4M7; -.
PaxDb; Q8W4M7; -.
PRIDE; Q8W4M7; -.
EnsemblPlants; AT1G03190.1; AT1G03190.1; AT1G03190.
EnsemblPlants; AT1G03190.2; AT1G03190.2; AT1G03190.
GeneID; 839557; -.
Gramene; AT1G03190.1; AT1G03190.1; AT1G03190.
Gramene; AT1G03190.2; AT1G03190.2; AT1G03190.
KEGG; ath:AT1G03190; -.
Araport; AT1G03190; -.
TAIR; locus:2014525; AT1G03190.
eggNOG; KOG1131; Eukaryota.
eggNOG; COG1199; LUCA.
HOGENOM; HOG000205390; -.
InParanoid; Q8W4M7; -.
KO; K10844; -.
OMA; PSVVRNY; -.
OrthoDB; EOG093602H1; -.
PhylomeDB; Q8W4M7; -.
Reactome; R-ATH-113418; Formation of the Early Elongation Complex.
Reactome; R-ATH-5696395; Formation of Incision Complex in GG-NER.
Reactome; R-ATH-5696400; Dual Incision in GG-NER.
Reactome; R-ATH-674695; RNA Polymerase II Pre-transcription Events.
Reactome; R-ATH-6781823; Formation of TC-NER Pre-Incision Complex.
Reactome; R-ATH-6782135; Dual incision in TC-NER.
Reactome; R-ATH-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
Reactome; R-ATH-6796648; TP53 Regulates Transcription of DNA Repair Genes.
Reactome; R-ATH-72086; mRNA Capping.
Reactome; R-ATH-73776; RNA Polymerase II Promoter Escape.
Reactome; R-ATH-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
Reactome; R-ATH-75953; RNA Polymerase II Transcription Initiation.
Reactome; R-ATH-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
Reactome; R-ATH-77075; RNA Pol II CTD phosphorylation and interaction with CE.
PRO; PR:Q8W4M7; -.
Proteomes; UP000006548; Chromosome 1.
ExpressionAtlas; Q8W4M7; baseline and differential.
Genevisible; Q8W4M7; AT.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004003; F:ATP-dependent DNA helicase activity; IEA:InterPro.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006281; P:DNA repair; IMP:TAIR.
GO; GO:0006289; P:nucleotide-excision repair; IEA:InterPro.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0009408; P:response to heat; IMP:TAIR.
GO; GO:0009411; P:response to UV; IMP:TAIR.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
InterPro; IPR006555; ATP-dep_Helicase_C.
InterPro; IPR010614; DEAD_2.
InterPro; IPR002464; DNA/RNA_helicase_DEAH_CS.
InterPro; IPR013020; DNA_helicase_DNA-repair_Rad3.
InterPro; IPR010643; HBB.
InterPro; IPR014013; Helic_SF1/SF2_ATP-bd_DinG/Rad3.
InterPro; IPR006554; Helicase-like_DEXD_c2.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR001945; RAD3/XPD.
PANTHER; PTHR11472:SF1; PTHR11472:SF1; 1.
Pfam; PF06733; DEAD_2; 1.
Pfam; PF06777; HBB; 1.
Pfam; PF13307; Helicase_C_2; 1.
PRINTS; PR00852; XRODRMPGMNTD.
SMART; SM00488; DEXDc2; 1.
SMART; SM00491; HELICc2; 1.
SUPFAM; SSF52540; SSF52540; 4.
TIGRFAMs; TIGR00604; rad3; 1.
PROSITE; PS00690; DEAH_ATP_HELICASE; 1.
PROSITE; PS51193; HELICASE_ATP_BIND_2; 1.
1: Evidence at protein level;
4Fe-4S; ATP-binding; Complete proteome; DNA damage; DNA repair;
DNA-binding; Helicase; Hydrolase; Iron; Iron-sulfur; Metal-binding;
Nucleotide-binding; Nucleus; Reference proteome; Transcription;
Transcription regulation.
CHAIN 1 758 DNA repair helicase XPD.
/FTId=PRO_0000101982.
DOMAIN 7 285 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
NP_BIND 42 49 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
MOTIF 234 238 DEAH box.
METAL 116 116 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 134 134 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 155 155 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 190 190 Iron-sulfur (4Fe-4S). {ECO:0000250}.
MUTAGEN 521 521 G->E: In uvh6-1; confers increased
sensitivity to UV light and heat, yellow-
green leaf coloration, and mild growth
defects. {ECO:0000269|PubMed:12857822}.
CONFLICT 559 559 K -> E (in Ref. 2; AAF14582).
{ECO:0000305}.
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


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