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Protein

DNA repair helicase RAD3

Gene

RAD3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

ATP-dependent DNA helicase involved in excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Necessary for excision of pyrimidine dimers. Also unwinds DNA/RNA duplexes. Plays an essential role in the cell viability. Involved in the maintenance of the fidelity of DNA replication. Acts as component of the general transcription and DNA repair factor IIH (TFIIH) core, which is essential for both basal and activated transcription, and is involved in nucleotide excision repair (NER) of damaged DNA. TFIIH has CTD kinase and DNA-dependent ATPase activity, and is essential for polymerase II transcription in vitro.2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi115 – 1151Iron-sulfur (4Fe-4S)By similarity
Metal bindingi133 – 1331Iron-sulfur (4Fe-4S)By similarity
Metal bindingi156 – 1561Iron-sulfur (4Fe-4S)By similarity
Metal bindingi191 – 1911Iron-sulfur (4Fe-4S)By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi42 – 498ATPPROSITE-ProRule annotation

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
  • damaged DNA binding Source: SGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • nucleotide-excision repair, DNA incision Source: SGD
  • phosphorylation of RNA polymerase II C-terminal domain Source: SGD
  • positive regulation of mitotic recombination Source: SGD
  • regulation of mitotic recombination Source: SGD
  • regulation of transposition, RNA-mediated Source: SGD
  • small molecule metabolic process Source: Reactome
  • transcription from RNA polymerase II promoter Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

DNA damage, DNA repair, Transcription, Transcription regulation

Keywords - Ligandi

4Fe-4S, ATP-binding, DNA-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-2564830. Cytosolic iron-sulfur cluster assembly.
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:
DNA repair helicase RAD3 (EC:3.6.4.12)
Alternative name(s):
General transcription and DNA repair factor IIH subunit RAD3
Short name:
TFIIH 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

EuPathDBiFungiDB:YER171W.
SGDiS000000973. RAD3.

Subcellular locationi

GO - Cellular componenti

  • core TFIIH complex Source: SGD
  • cytosol Source: Reactome
  • holo TFIIH complex Source: SGD
  • nucleotide-excision repair factor 3 complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi48 – 481K → R or A: Abolishes ATPase and DNA helicase activities but not ATP-binding capacity. 3 Publications
Mutagenesisi111 – 1111R → H: Confers an UV-sensitive phenotype. 1 Publication
Mutagenesisi115 – 1151C → S: Confers an UV-sensitive phenotype. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 778778DNA repair helicase RAD3PRO_0000101983Add
BLAST

Proteomic databases

MaxQBiP06839.

Interactioni

Subunit structurei

Component of the TFIIH core complex, which is composed of RAD3, SSL1, SSL2, TFB1, TFB2, TFB4 and TFB5.2 Publications

Protein-protein interaction databases

BioGridi36924. 166 interactions.
DIPiDIP-2425N.
IntActiP06839. 28 interactions.
MINTiMINT-617451.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5FMFelectron microscopy6.00Y1-778[»]
ProteinModelPortaliP06839.
SMRiP06839. Positions 455-686.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 285279Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi235 – 2384DEAH box

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi759 – 77820Asp/Glu-rich (acidic)Add
BLAST

Sequence similaritiesi

Belongs to the helicase family. RAD3/XPD subfamily.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00550000075092.
HOGENOMiHOG000205390.
InParanoidiP06839.
KOiK10844.
OMAiDEVWKYK.
OrthoDBiEOG7BKD38.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR006555. ATP-dep_Helicase_C.
IPR010614. DEAD_2.
IPR002464. DNA/RNA_helicase_DEAH_CS.
IPR013020. DNA_helicase_DNA-repair_Rad3.
IPR010643. HBB.
IPR014013. Helic_SF1/SF2_ATP-bd_DinG/Rad3.
IPR006554. Helicase-like_DEXD_c2.
IPR027417. P-loop_NTPase.
IPR001945. RAD3/XPD.
[Graphical view]
PfamiPF06733. DEAD_2. 1 hit.
PF06777. HBB. 1 hit.
PF13307. Helicase_C_2. 1 hit.
[Graphical view]
PRINTSiPR00852. XRODRMPGMNTD.
SMARTiSM00488. DEXDc2. 1 hit.
SM00491. HELICc2. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 6 hits.
TIGRFAMsiTIGR00604. rad3. 1 hit.
PROSITEiPS00690. DEAH_ATP_HELICASE. 1 hit.
PS51193. HELICASE_ATP_BIND_2. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti2 – 21K → G AA sequence (PubMed:8269516).Curated

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.

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
EntryMethodResolution (Å)ChainPositionsPDBsum
5FMFelectron microscopy6.00Y1-778[»]
ProteinModelPortaliP06839.
SMRiP06839. Positions 455-686.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36924. 166 interactions.
DIPiDIP-2425N.
IntActiP06839. 28 interactions.
MINTiMINT-617451.

Proteomic databases

MaxQBiP06839.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER171W; YER171W; YER171W.
GeneIDi856918.
KEGGisce:YER171W.

Organism-specific databases

EuPathDBiFungiDB:YER171W.
SGDiS000000973. RAD3.

Phylogenomic databases

GeneTreeiENSGT00550000075092.
HOGENOMiHOG000205390.
InParanoidiP06839.
KOiK10844.
OMAiDEVWKYK.
OrthoDBiEOG7BKD38.

Enzyme and pathway databases

BioCyciYEAST:G3O-30331-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-2564830. Cytosolic iron-sulfur cluster assembly.
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

PROiP06839.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR006555. ATP-dep_Helicase_C.
IPR010614. DEAD_2.
IPR002464. DNA/RNA_helicase_DEAH_CS.
IPR013020. DNA_helicase_DNA-repair_Rad3.
IPR010643. HBB.
IPR014013. Helic_SF1/SF2_ATP-bd_DinG/Rad3.
IPR006554. Helicase-like_DEXD_c2.
IPR027417. P-loop_NTPase.
IPR001945. RAD3/XPD.
[Graphical view]
PfamiPF06733. DEAD_2. 1 hit.
PF06777. HBB. 1 hit.
PF13307. Helicase_C_2. 1 hit.
[Graphical view]
PRINTSiPR00852. XRODRMPGMNTD.
SMARTiSM00488. DEXDc2. 1 hit.
SM00491. HELICc2. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 6 hits.
TIGRFAMsiTIGR00604. rad3. 1 hit.
PROSITEiPS00690. DEAH_ATP_HELICASE. 1 hit.
PS51193. HELICASE_ATP_BIND_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of the RAD3 gene of Saccharomyces cerevisiae: a potential adenine nucleotide binding amino acid sequence and a nonessential acidic carboxyl terminal region."
    Reynolds P., Higgins D.R., Prakash L., Prakash S.
    Nucleic Acids Res. 13:2357-2372(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "RAD3 gene of Saccharomyces cerevisiae: nucleotide sequence of wild-type and mutant alleles, transcript mapping, and aspects of gene regulation."
    Naumovski L., Chu G., Berg P., Friedberg E.C.
    Mol. Cell. Biol. 5:17-26(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Dual roles of a multiprotein complex from S. cerevisiae in transcription and DNA repair."
    Feaver W.J., Svejstrup J.Q., Bardwell L., Bardwell A.J., Buratowski S., Gulyas K.D., Donahue T.F., Friedberg E.C., Kornberg R.D.
    Cell 75:1379-1387(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-10.
  6. "Mutation of lysine-48 to arginine in the yeast RAD3 protein abolishes its ATPase and DNA helicase activities but not the ability to bind ATP."
    Sung P., Higgins D., Prakash L., Prakash S.
    EMBO J. 7:3263-3269(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF LYS-48.
  7. "DNA.RNA helicase activity of RAD3 protein of Saccharomyces cerevisiae."
    Bailly V., Sung P., Prakash L., Prakash S.
    Proc. Natl. Acad. Sci. U.S.A. 88:9712-9716(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF LYS-48.
  8. "Effects of multiple yeast rad3 mutant alleles on UV sensitivity, mutability, and mitotic recombination."
    Song J.M., Montelone B.A., Siede W., Friedberg E.C.
    J. Bacteriol. 172:6620-6630(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTANTS.
  9. "The RAD3 gene is a member of the DEAH family RNA helicase-like protein."
    Harosh I., Deschavanne P.J.
    Nucleic Acids Res. 19:6331-6331(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRESENCE OF A DEAH MOTIF.
  10. "RNA polymerase transcription factor IIH holoenzyme from yeast."
    Svejstrup J.Q., Feaver W.J., LaPointe J., Kornberg R.D.
    J. Biol. Chem. 269:28044-28048(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF TFIIH IN RNA POLYMERASE II TRANSCRIPTION, IDENTIFICATION IN THE TFIIH COMPLEX.
  11. "Reconstitution of TFIIH and requirement of its DNA helicase subunits, Rad3 and Rad25, in the incision step of nucleotide excision repair."
    Sung P., Guzder S.N., Prakash L., Prakash S.
    J. Biol. Chem. 271:10821-10826(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE TFIIH CORE COMPLEX IN DNA REPAIR.
  12. "Revised subunit structure of yeast transcription factor IIH (TFIIH) and reconciliation with human TFIIH."
    Takagi Y., Komori H., Chang W.-H., Hudmon A., Erdjument-Bromage H., Tempst P., Kornberg R.D.
    J. Biol. Chem. 278:43897-43900(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE TFIIH CORE COMPLEX.
  13. "The Rad3 protein from Saccharomyces cerevisiae: a DNA and DNA:RNA helicase with putative RNA helicase activity."
    Deschavanne P.J., Harosh I.
    Mol. Microbiol. 7:831-835(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  14. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  15. "The DNA repair helicases XPD and FancJ have essential iron-sulfur domains."
    Rudolf J., Makrantoni V., Ingledew W.J., Stark M.J., White M.F.
    Mol. Cell 23:801-808(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: COFACTOR, IRON-SULFUR-BINDING, MUTAGENESIS OF LYS-48; ARG-111 AND CYS-115.

Entry informationi

Entry nameiRAD3_YEAST
AccessioniPrimary (citable) accession number: P06839
Secondary accession number(s): D3DM79
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: July 6, 2016
This is version 169 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

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

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.