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Protein

General transcription and DNA repair factor IIH helicase subunit XPD

Gene

RAD3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's 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/RAD3 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/RAD3 acts by forming a bridge between TFIIK and the core-TFIIH complex. Involved in the maintenance of the fidelity of DNA replication.4 Publications

Miscellaneous

Present with 14400 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

[4Fe-4S] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi115Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi133Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi156Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi191Iron-sulfur (4Fe-4S)By similarity1

Regions

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

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: UniProtKB
  • 5'-3' DNA helicase activity Source: UniProtKB
  • ATP binding Source: UniProtKB-KW
  • ATP-dependent 5'-3' DNA helicase activity Source: SGD
  • ATP-dependent DNA helicase activity Source: GO_Central
  • damaged DNA binding Source: SGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

BioCyciYEAST:G3O-30331-MONOMER
ReactomeiR-SCE-113418 Formation of the Early Elongation Complex
R-SCE-2564818 Cytosolic iron-sulfur cluster assembly (yeast)
R-SCE-5696395 Formation of Incision Complex in GG-NER
R-SCE-5696400 Dual Incision in GG-NER
R-SCE-674695 RNA Polymerase II Pre-transcription Events
R-SCE-6781823 Formation of TC-NER Pre-Incision Complex
R-SCE-6782135 Dual incision in TC-NER
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SCE-72086 mRNA Capping
R-SCE-73776 RNA Polymerase II Promoter Escape
R-SCE-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SCE-75953 RNA Polymerase II Transcription Initiation
R-SCE-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SCE-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
RNA polymerase II transcription factor B subunit RAD3
Short name:
TFB subunit RAD3
Gene namesi
Name:RAD3
Synonyms:REM1
Ordered Locus Names:YER171W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

SGDiS000000973 RAD3

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi48K → R or A: Abolishes ATPase and DNA helicase activities but not ATP-binding capacity. 3 Publications1
Mutagenesisi111R → H: Confers an UV-sensitive phenotype. 1 Publication1
Mutagenesisi115C → S: Confers an UV-sensitive phenotype. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001019831 – 778General transcription and DNA repair factor IIH helicase subunit XPDAdd BLAST778

Proteomic databases

MaxQBiP06839
PaxDbiP06839
PRIDEiP06839

Interactioni

Subunit structurei

Component of the 7-subunit TFIIH core complex composed of XPB/SSL2, XPD/RAD3, 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 CCL1, KIN28 and TFB3 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription.3 Publications

Protein-protein interaction databases

BioGridi36924, 188 interactors
ComplexPortaliCPX-1659 General transcription factor complex TFIIH
DIPiDIP-2425N
IntActiP06839, 71 interactors
MINTiP06839
STRINGi4932.YER171W

Structurei

3D structure databases

ProteinModelPortaliP06839
SMRiP06839
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini7 – 285Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST279

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi235 – 238DEAH box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi759 – 778Asp/Glu-rich (acidic)Add BLAST20

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00550000075092
HOGENOMiHOG000205390
InParanoidiP06839
KOiK10844
OMAiKKPLRFC
OrthoDBiEOG092C28I3

Family and domain databases

InterProiView protein in InterPro
IPR006555 ATP-dep_Helicase_C
IPR010614 DEAD_2
IPR002464 DNA/RNA_helicase_DEAH_CS
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, 2 hits
TIGRFAMsiTIGR00604 rad3, 1 hit
PROSITEiView protein in PROSITE
PS00690 DEAH_ATP_HELICASE, 1 hit
PS51193 HELICASE_ATP_BIND_2, 1 hit

Sequencei

Sequence statusi: Complete.

P06839-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV
60 70 80 90 100
SLLSLTIAYQ MHYPEHRKII YCSRTMSEIE KALVELENLM DYRTKELGYQ
110 120 130 140 150
EDFRGLGLTS RKNLCLHPEV SKERKGTVVD EKCRRMTNGQ AKRKLEEDPE
160 170 180 190 200
ANVELCEYHE NLYNIEVEDY LPKGVFSFEK LLKYCEEKTL CPYFIVRRMI
210 220 230 240 250
SLCNIIIYSY HYLLDPKIAE RVSNEVSKDS IVIFDEAHNI DNVCIESLSL
260 270 280 290 300
DLTTDALRRA TRGANALDER ISEVRKVDSQ KLQDEYEKLV QGLHSADILT
310 320 330 340 350
DQEEPFVETP VLPQDLLTEA IPGNIRRAEH FVSFLKRLIE YLKTRMKVLH
360 370 380 390 400
VISETPKSFL QHLKQLTFIE RKPLRFCSER LSLLVRTLEV TEVEDFTALK
410 420 430 440 450
DIATFATLIS TYEEGFLLII EPYEIENAAV PNPIMRFTCL DASIAIKPVF
460 470 480 490 500
ERFSSVIITS GTISPLDMYP RMLNFKTVLQ KSYAMTLAKK SFLPMIITKG
510 520 530 540 550
SDQVAISSRF EIRNDPSIVR NYGSMLVEFA KITPDGMVVF FPSYLYMESI
560 570 580 590 600
VSMWQTMGIL DEVWKHKLIL VETPDAQETS LALETYRKAC SNGRGAILLS
610 620 630 640 650
VARGKVSEGI DFDHQYGRTV LMIGIPFQYT ESRILKARLE FMRENYRIRE
660 670 680 690 700
NDFLSFDAMR HAAQCLGRVL RGKDDYGVMV LADRRFSRKR SQLPKWIAQG
710 720 730 740 750
LSDADLNLST DMAISNTKQF LRTMAQPTDP KDQEGVSVWS YEDLIKHQNS
760 770
RKDQGGFIEN ENKEGEQDED EDEDIEMQ
Length:778
Mass (Da):89,786
Last modified:January 1, 1988 - v1
Checksum:i978BCA01751949B4
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti2K → G AA sequence (PubMed:8269516).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02368 Genomic DNA Translation: CAA26215.1
K03293 Genomic DNA Translation: AAA34943.1
U18922 Genomic DNA Translation: AAB64698.1
BK006939 Genomic DNA Translation: DAA07833.1
PIRiA23308
RefSeqiNP_011098.3, NM_001179061.3

Genome annotation databases

EnsemblFungiiYER171W; YER171W; YER171W
GeneIDi856918
KEGGisce:YER171W

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02368 Genomic DNA Translation: CAA26215.1
K03293 Genomic DNA Translation: AAA34943.1
U18922 Genomic DNA Translation: AAB64698.1
BK006939 Genomic DNA Translation: DAA07833.1
PIRiA23308
RefSeqiNP_011098.3, NM_001179061.3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FMFelectron microscopy6.00Y1-778[»]
5OQJelectron microscopy4.7001-778[»]
5OQMelectron microscopy5.8001-778[»]
5SVAelectron microscopy15.30Y1-778[»]
ProteinModelPortaliP06839
SMRiP06839
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36924, 188 interactors
ComplexPortaliCPX-1659 General transcription factor complex TFIIH
DIPiDIP-2425N
IntActiP06839, 71 interactors
MINTiP06839
STRINGi4932.YER171W

Proteomic databases

MaxQBiP06839
PaxDbiP06839
PRIDEiP06839

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER171W; YER171W; YER171W
GeneIDi856918
KEGGisce:YER171W

Organism-specific databases

SGDiS000000973 RAD3

Phylogenomic databases

GeneTreeiENSGT00550000075092
HOGENOMiHOG000205390
InParanoidiP06839
KOiK10844
OMAiKKPLRFC
OrthoDBiEOG092C28I3

Enzyme and pathway databases

BioCyciYEAST:G3O-30331-MONOMER
ReactomeiR-SCE-113418 Formation of the Early Elongation Complex
R-SCE-2564818 Cytosolic iron-sulfur cluster assembly (yeast)
R-SCE-5696395 Formation of Incision Complex in GG-NER
R-SCE-5696400 Dual Incision in GG-NER
R-SCE-674695 RNA Polymerase II Pre-transcription Events
R-SCE-6781823 Formation of TC-NER Pre-Incision Complex
R-SCE-6782135 Dual incision in TC-NER
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SCE-72086 mRNA Capping
R-SCE-73776 RNA Polymerase II Promoter Escape
R-SCE-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SCE-75953 RNA Polymerase II Transcription Initiation
R-SCE-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SCE-77075 RNA Pol II CTD phosphorylation and interaction with CE

Miscellaneous databases

PROiPR:P06839

Family and domain databases

InterProiView protein in InterPro
IPR006555 ATP-dep_Helicase_C
IPR010614 DEAD_2
IPR002464 DNA/RNA_helicase_DEAH_CS
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, 2 hits
TIGRFAMsiTIGR00604 rad3, 1 hit
PROSITEiView protein in PROSITE
PS00690 DEAH_ATP_HELICASE, 1 hit
PS51193 HELICASE_ATP_BIND_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRAD3_YEAST
AccessioniPrimary (citable) accession number: P06839
Secondary accession number(s): D3DM79
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: November 7, 2018
This is version 190 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome V
    Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names
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Main funding by: National Institutes of Health

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