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Protein

General transcription and DNA repair factor IIH helicase subunit XPD

Gene

rad15

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

ATP-dependent 5'-3' DNA helicase, component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to TFIIK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. The ATP-dependent helicase activity of XPD/rad15 is required for DNA opening. In transcription, TFIIH has an essential role in transcription initiation. When the pre-initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module TFIIK controls the initiation of transcription. XPD/rad15 acts by forming a bridge between TFIIK and the core-TFIIH complex. Involved in the maintenance of the fidelity of DNA replication.2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.By similarity

Cofactori

[4Fe-4S] clusterBy similarityNote: Binds 1 [4Fe-4S] cluster.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi115Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi133Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi154Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi189Iron-sulfur (4Fe-4S)By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi42 – 49ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

  • nucleotide-excision repair, DNA duplex unwinding Source: PomBase
  • transcription initiation from RNA polymerase II promoter Source: PomBase

Keywordsi

Molecular functionDNA-binding, Helicase, Hydrolase
Biological processDNA damage, DNA repair
Ligand4Fe-4S, ATP-binding, Iron, Iron-sulfur, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-SPO-113418 Formation of the Early Elongation Complex
R-SPO-5696395 Formation of Incision Complex in GG-NER
R-SPO-5696400 Dual Incision in GG-NER
R-SPO-674695 RNA Polymerase II Pre-transcription Events
R-SPO-6781823 Formation of TC-NER Pre-Incision Complex
R-SPO-6782135 Dual incision in TC-NER
R-SPO-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SPO-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SPO-72086 mRNA Capping
R-SPO-73776 RNA Polymerase II Promoter Escape
R-SPO-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SPO-75953 RNA Polymerase II Transcription Initiation
R-SPO-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SPO-77075 RNA Pol II CTD phosphorylation and interaction with CE

Names & Taxonomyi

Protein namesi
Recommended name:
General transcription and DNA repair factor IIH helicase subunit XPD (EC:3.6.4.12)
Short name:
TFIIH subunit XPD
Alternative name(s):
DNA repair helicase RAD3 homolog1 Publication
Short name:
Protein rhp31 Publication
DNA repair helicase rad151 Publication
RNA polymerase II transcription factor B subunit rad15
Short name:
TFB subunit rad15
Gene namesi
Name:rad151 Publication
Synonyms:rad51 Publication, rhp31 Publication
ORF Names:SPAC1D4.12Imported
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome I

Organism-specific databases

EuPathDBiFungiDB:SPAC1D4.12
PomBaseiSPAC1D4.12 rad15

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001019841 – 772General transcription and DNA repair factor IIH helicase subunit XPDAdd BLAST772

Proteomic databases

MaxQBiP26659
PaxDbiP26659
PRIDEiP26659

Interactioni

Subunit structurei

Component of the 7-subunit TFIIH core complex composed of XPB/ptr8, XPD/rad15, ssl1, tfb1, tfb2, tfb4 and tfb5, which is active in NER. The core complex associates with the 3-subunit CTD-kinase module TFIIK composed of mcs2/cyclin H, mcs6/cdk7 and pmh1/tfb3 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription.1 Publication

Protein-protein interaction databases

IntActiP26659, 1 interactor
STRINGi4896.SPAC1D4.12.1

Structurei

3D structure databases

ProteinModelPortaliP26659
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini7 – 283Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST277

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi233 – 236DEAH box4

Sequence similaritiesi

Belongs to the helicase family. RAD3/XPD subfamily.Curated

Phylogenomic databases

HOGENOMiHOG000205390
InParanoidiP26659
KOiK10844
OMAiPSVVRNY
OrthoDBiEOG092C28I3
PhylomeDBiP26659

Family and domain databases

InterProiView protein in InterPro
IPR006555 ATP-dep_Helicase_C
IPR010614 DEAD_2
IPR010643 HBB
IPR014013 Helic_SF1/SF2_ATP-bd_DinG/Rad3
IPR006554 Helicase-like_DEXD_c2
IPR027417 P-loop_NTPase
IPR013020 Rad3/Chl1-like
IPR001945 RAD3/XPD
PANTHERiPTHR11472:SF1 PTHR11472:SF1, 1 hit
PfamiView protein in Pfam
PF06733 DEAD_2, 1 hit
PF06777 HBB, 1 hit
PF13307 Helicase_C_2, 1 hit
PRINTSiPR00852 XRODRMPGMNTD
SMARTiView protein in SMART
SM00488 DEXDc2, 1 hit
SM00491 HELICc2, 1 hit
SUPFAMiSSF52540 SSF52540, 6 hits
TIGRFAMsiTIGR00604 rad3, 1 hit
PROSITEiView protein in PROSITE
PS51193 HELICASE_ATP_BIND_2, 1 hit

Sequencei

Sequence statusi: Complete.

P26659-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFYIDDLPI LFPYPRIYPE QYQYMCDLKH SLDAGGIALL EMPSGTGKTI
60 70 80 90 100
SLLSLIVSYQ QHYPEHRKLI YCSRTMSEID KALAELKRLM AYRTSQLGYE
110 120 130 140 150
EPFLGLGLTS RKNLCLHPSV RREKNGNVVD ARCRSLTAGF VREQRLAGMD
160 170 180 190 200
VPTCEFHDNL EDLEPHSLIS NGVWTLDDIT EYGEKTTRCP YFTVRRMLPF
210 220 230 240 250
CNVIIYSYHY LLDPKIAERV SRELSKDCIV VFDEAHNIDN VCIESLSIDL
260 270 280 290 300
TESSLRKASK SILSLEQKVN EVKQSDSKKL QDEYQKLVRG LQDANAANDE
310 320 330 340 350
DQFMANPVLP EDVLKEAVPG NIRRAEHFIA FLKRFVEYLK TRMKVLHVIA
360 370 380 390 400
ETPTSFLQHV KDITFIDKKP LRFCAERLTS LVRALQISLV EDFHSLQQVV
410 420 430 440 450
AFATLVATYE RGFILILEPF ETENATVPNP ILRFSCLDAS IAIKPVFERF
460 470 480 490 500
RSVIITSGTL SPLDMYPKML QFNTVMQESY GMSLARNCFL PMVVTRGSDQ
510 520 530 540 550
VAISSKFEAR NDPSVVRNYG NILVEFSKIT PDGLVAFFPS YLYLESIVSS
560 570 580 590 600
WQSMGILDEV WKYKLILVET PDPHETTLAL ETYRAACSNG RGAVLLSVAR
610 620 630 640 650
GKVSEGVDFD HHYGRAVIMF GIPYQYTESR VLKARLEFLR DTYQIREADF
660 670 680 690 700
LTFDAMRHAA QCLGRVLRGK DDHGIMVLAD KRYGRSDKRT KLPKWIQQYI
710 720 730 740 750
TEGATNLSTD MSLALAKKFL RTMAQPFTAS DQEGISWWSL DDLLIHQKKA
760 770
LKSAAIEQSK HEDEMDIDVV ET
Length:772
Mass (Da):88,149
Last modified:October 1, 1996 - v2
Checksum:iA21025C298A28F08
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti225S → N in CAA45870 (PubMed:1534406).Curated1
Sequence conflicti588S → T in CAA43022 (PubMed:1319571).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X64583 Genomic DNA Translation: CAA45870.1
X60499 Genomic DNA Translation: CAA43022.1
CU329670 Genomic DNA Translation: CAA93221.1
PIRiS22660
RefSeqiNP_593025.1, NM_001018424.2

Genome annotation databases

EnsemblFungiiSPAC1D4.12.1; SPAC1D4.12.1:pep; SPAC1D4.12
GeneIDi2542203
KEGGispo:SPAC1D4.12

Similar proteinsi

Entry informationi

Entry nameiRAD15_SCHPO
AccessioniPrimary (citable) accession number: P26659
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: October 1, 1996
Last modified: March 28, 2018
This is version 147 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families
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