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Protein

DNA repair helicase RAD25

Gene

SSL2

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

Probably an ATP-dependent DNA helicase, which may have a DNA unwinding function. Has an essential function in translation initiation. 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.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi386 – 393ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent DNA helicase activity Source: SGD
  • DNA binding Source: UniProtKB-KW
  • DNA translocase activity Source: SGD

GO - Biological processi

  • DNA duplex unwinding Source: SGD
  • nucleotide-excision repair, DNA incision Source: SGD
  • phosphorylation of RNA polymerase II C-terminal domain Source: SGD
  • poly(A)+ mRNA export from nucleus Source: SGD
  • promoter clearance from RNA polymerase II promoter Source: SGD
  • regulation of mitotic recombination Source: SGD
  • regulation of transposition, RNA-mediated Source: SGD
  • transcriptional open complex formation at RNA polymerase II promoter Source: SGD
  • transcription from RNA polymerase II promoter Source: SGD
  • transcription initiation 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

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31393-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
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 RAD25 (EC:3.6.4.12)
Alternative name(s):
General transcription and DNA repair factor IIH subunit RAD25
Short name:
TFIIH subunit RAD25
Suppressor of stem-loop mutation 2
Gene namesi
Name:SSL2
Synonyms:LOM3, RAD25, UVS112
Ordered Locus Names:YIL143C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IX

Organism-specific databases

EuPathDBiFungiDB:YIL143C.
SGDiS000001405. SSL2.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • holo TFIIH complex Source: SGD
  • nucleotide-excision repair factor 3 complex Source: SGD
  • nucleus Source: SGD
  • transcriptional preinitiation complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001019941 – 843DNA repair helicase RAD25Add BLAST843

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei752PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ00578.
PRIDEiQ00578.
TopDownProteomicsiQ00578.

PTM databases

iPTMnetiQ00578.

Interactioni

Subunit structurei

Component of the TFIIH core complex, which is composed of RAD3, SSL1, SSL2, TFB1, TFB2, TFB4 and TFB5.1 Publication

Protein-protein interaction databases

BioGridi34849. 36 interactors.
DIPiDIP-731N.
IntActiQ00578. 17 interactors.
MINTiMINT-573804.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FMFelectron microscopy6.001294-785[»]
5SVAelectron microscopy15.30Z1-843[»]
ProteinModelPortaliQ00578.
SMRiQ00578.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini373 – 535Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST163
Domaini589 – 743Helicase C-terminalPROSITE-ProRule annotationAdd BLAST155

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi64 – 75Nuclear localization signalSequence analysisAdd BLAST12
Motifi487 – 491DEVH box5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi302 – 309Asp/Glu-rich (acidic)8

Sequence similaritiesi

Belongs to the helicase family. RAD25/XPB subfamily.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000002204.
HOGENOMiHOG000160172.
InParanoidiQ00578.
KOiK10843.
OMAiGSFGSRQ.
OrthoDBiEOG092C0I1P.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR032438. ERCC3_RAD25_C.
IPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR001161. XPB/Ssl2.
IPR032830. XPB/Ssl2_N.
[Graphical view]
PfamiPF16203. ERCC3_RAD25_C. 1 hit.
PF13625. Helicase_C_3. 1 hit.
PF04851. ResIII. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
TIGRFAMsiTIGR00603. rad25. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q00578-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG
60 70 80 90 100
RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKDK ALLQDTNSDI
110 120 130 140 150
PADFVPDSVS GMFRSHDFSY LRLRPDHASR PLWISPSDGR IILESFSPLA
160 170 180 190 200
EQAQDFLVTI AEPISRPSHI HEYKITAYSL YAAVSVGLET DDIISVLDRL
210 220 230 240 250
SKVPVAESII NFIKGATISY GKVKLVIKHN RYFVETTQAD ILQMLLNDSV
260 270 280 290 300
IGPLRIDSDH QVQPPEDVLQ QQLQQTAGKP ATNVNPNDVE AVFSAVIGGD
310 320 330 340 350
NEREEEDDDI DAVHSFEIAN ESVEVVKKRC QEIDYPVLEE YDFRNDHRNP
360 370 380 390 400
DLDIDLKPST QIRPYQEKSL SKMFGNGRAR SGIIVLPCGA GKTLVGITAA
410 420 430 440 450
CTIKKSVIVL CTSSVSVMQW RQQFLQWCTL QPENCAVFTS DNKEMFQTES
460 470 480 490 500
GLVVSTYSMV ANTRNRSHDS QKVMDFLTGR EWGFIILDEV HVVPAAMFRR
510 520 530 540 550
VVSTIAAHAK LGLTATLVRE DDKIGDLNFL IGPKLYEANW MELSQKGHIA
560 570 580 590 600
NVQCAEVWCP MTAEFYQEYL RETARKRMLL YIMNPTKFQA CQFLIQYHER
610 620 630 640 650
RGDKIIVFSD NVYALQEYAL KMGKPFIYGS TPQQERMNIL QNFQYNDQIN
660 670 680 690 700
TIFLSKVGDT SIDLPEATCL IQISSHYGSR RQEAQRLGRI LRAKRRNDEG
710 720 730 740 750
FNAFFYSLVS KDTQEMYYST KRQAFLVDQG YAFKVITHLH GMENIPNLAY
760 770 780 790 800
ASPRERRELL QEVLLKNEEA AGIEVGDDAD NSVGRGSNGH KRFKSKAVRG
810 820 830 840
EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN LKK
Length:843
Mass (Da):95,341
Last modified:April 1, 1993 - v1
Checksum:iFA4013E8156FE1C5
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti9P → S in AAA34942 (PubMed:1333609).Curated1
Sequence conflicti48S → L in AAA34942 (PubMed:1333609).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti427W → L in suppressor mutant. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38059 Genomic DNA. Translation: CAA86135.1.
M94176 Genomic DNA. Translation: AAA35102.1.
L01414 Genomic DNA. Translation: AAA34942.1.
AY692883 Genomic DNA. Translation: AAT92902.1.
BK006942 Genomic DNA. Translation: DAA08410.1.
PIRiS31272.
RefSeqiNP_012123.1. NM_001179491.1.

Genome annotation databases

EnsemblFungiiYIL143C; YIL143C; YIL143C.
GeneIDi854663.
KEGGisce:YIL143C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38059 Genomic DNA. Translation: CAA86135.1.
M94176 Genomic DNA. Translation: AAA35102.1.
L01414 Genomic DNA. Translation: AAA34942.1.
AY692883 Genomic DNA. Translation: AAT92902.1.
BK006942 Genomic DNA. Translation: DAA08410.1.
PIRiS31272.
RefSeqiNP_012123.1. NM_001179491.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FMFelectron microscopy6.001294-785[»]
5SVAelectron microscopy15.30Z1-843[»]
ProteinModelPortaliQ00578.
SMRiQ00578.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34849. 36 interactors.
DIPiDIP-731N.
IntActiQ00578. 17 interactors.
MINTiMINT-573804.

PTM databases

iPTMnetiQ00578.

Proteomic databases

MaxQBiQ00578.
PRIDEiQ00578.
TopDownProteomicsiQ00578.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYIL143C; YIL143C; YIL143C.
GeneIDi854663.
KEGGisce:YIL143C.

Organism-specific databases

EuPathDBiFungiDB:YIL143C.
SGDiS000001405. SSL2.

Phylogenomic databases

GeneTreeiENSGT00390000002204.
HOGENOMiHOG000160172.
InParanoidiQ00578.
KOiK10843.
OMAiGSFGSRQ.
OrthoDBiEOG092C0I1P.

Enzyme and pathway databases

BioCyciYEAST:G3O-31393-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
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

PROiQ00578.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR032438. ERCC3_RAD25_C.
IPR006935. Helicase/UvrB_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR001161. XPB/Ssl2.
IPR032830. XPB/Ssl2_N.
[Graphical view]
PfamiPF16203. ERCC3_RAD25_C. 1 hit.
PF13625. Helicase_C_3. 1 hit.
PF04851. ResIII. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
TIGRFAMsiTIGR00603. rad25. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRAD25_YEAST
AccessioniPrimary (citable) accession number: Q00578
Secondary accession number(s): D6VVE4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: April 1, 1993
Last modified: November 30, 2016
This is version 164 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

A C-terminal deletion renders yeast hypersensitive to UV light.
Present with 825 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, 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 IX
    Yeast (Saccharomyces cerevisiae) chromosome IX: 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.