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Protein

ATP-dependent RNA helicase DBP3

Gene

DBP3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

ATP-dependent RNA helicase required for 60S ribosomal subunit synthesis. Involved in efficient pre-rRNA processing, predominantly at site A3, which is necessary for the normal formation of 25S and 5.8S rRNAs.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi156 – 1638ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: SGD
  • RNA binding Source: UniProtKB-KW
  • RNA-dependent ATPase activity Source: SGD

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30579-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DBP3 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 3
Helicase CA3
Gene namesi
Name:DBP3
Ordered Locus Names:YGL078C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome VII

Organism-specific databases

CYGDiYGL078c.
EuPathDBiFungiDB:YGL078C.
SGDiS000003046. DBP3.

Subcellular locationi

GO - Cellular componenti

  • nucleolus Source: SGD
  • preribosome, large subunit precursor Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 523523ATP-dependent RNA helicase DBP3PRO_0000055017Add
BLAST

Proteomic databases

MaxQBiP20447.
PaxDbiP20447.
PeptideAtlasiP20447.

Interactioni

Protein-protein interaction databases

BioGridi33172. 116 interactions.
DIPiDIP-2668N.
IntActiP20447. 10 interactions.
MINTiMINT-1164200.

Structurei

3D structure databases

ProteinModelPortaliP20447.
SMRiP20447. Positions 90-489.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini143 – 315173Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini344 – 493150Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi114 – 14027Q motifAdd
BLAST
Motifi262 – 2654DEAD box

Domaini

The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.

Sequence similaritiesi

Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0513.
GeneTreeiENSGT00780000121987.
HOGENOMiHOG000268804.
InParanoidiP20447.
KOiK14811.
OMAiPIQSASW.
OrthoDBiEOG7TJ3T2.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P20447-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKEEIADKK RKVVDEEVIE KKKSKKHKKD KKDKKEKKDK KHKKHKKEKK
60 70 80 90 100
GEKEVEVPEK ESEKKPEPTS AVASEFYVQS EALTSLPQSD IDEYFKENEI
110 120 130 140 150
AVEDSLDLAL RPLLSFDYLS LDSSIQAEIS KFPKPTPIQA VAWPYLLSGK
160 170 180 190 200
DVVGVAETGS GKTFAFGVPA ISHLMNDQKK RGIQVLVISP TRELASQIYD
210 220 230 240 250
NLIVLTDKVG MQCCCVYGGV PKDEQRIQLK KSQVVVATPG RLLDLLQEGS
260 270 280 290 300
VDLSQVNYLV LDEADRMLEK GFEEDIKNII RETDASKRQT LMFTATWPKE
310 320 330 340 350
VRELASTFMN NPIKVSIGNT DQLTANKRIT QIVEVVDPRG KERKLLELLK
360 370 380 390 400
KYHSGPKKNE KVLIFALYKK EAARVERNLK YNGYNVAAIH GDLSQQQRTQ
410 420 430 440 450
ALNEFKSGKS NLLLATDVAA RGLDIPNVKT VINLTFPLTV EDYVHRIGRT
460 470 480 490 500
GRAGQTGTAH TLFTEQEKHL AGGLVNVLNG ANQPVPEDLI KFGTHTKKKE
510 520
HSAYGSFFKD VDLTKKPKKI TFD
Length:523
Mass (Da):58,827
Last modified:October 1, 1996 - v2
Checksum:iC198CF4E8D5BAFAA
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti441 – 4411E → A no nucleotide entry (PubMed:2406722).Curated
Sequence conflicti444 – 4441V → I no nucleotide entry (PubMed:2406722).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M80437 Genomic DNA. Translation: AAA73137.1.
Z72600 Genomic DNA. Translation: CAA96783.1.
BK006941 Genomic DNA. Translation: DAA08027.1.
PIRiS30805.
RefSeqiNP_011437.3. NM_001180943.3.

Genome annotation databases

EnsemblFungiiYGL078C; YGL078C; YGL078C.
GeneIDi852802.
KEGGisce:YGL078C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M80437 Genomic DNA. Translation: AAA73137.1.
Z72600 Genomic DNA. Translation: CAA96783.1.
BK006941 Genomic DNA. Translation: DAA08027.1.
PIRiS30805.
RefSeqiNP_011437.3. NM_001180943.3.

3D structure databases

ProteinModelPortaliP20447.
SMRiP20447. Positions 90-489.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33172. 116 interactions.
DIPiDIP-2668N.
IntActiP20447. 10 interactions.
MINTiMINT-1164200.

Proteomic databases

MaxQBiP20447.
PaxDbiP20447.
PeptideAtlasiP20447.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYGL078C; YGL078C; YGL078C.
GeneIDi852802.
KEGGisce:YGL078C.

Organism-specific databases

CYGDiYGL078c.
EuPathDBiFungiDB:YGL078C.
SGDiS000003046. DBP3.

Phylogenomic databases

eggNOGiCOG0513.
GeneTreeiENSGT00780000121987.
HOGENOMiHOG000268804.
InParanoidiP20447.
KOiK14811.
OMAiPIQSASW.
OrthoDBiEOG7TJ3T2.

Enzyme and pathway databases

BioCyciYEAST:G3O-30579-MONOMER.

Miscellaneous databases

NextBioi972321.
PROiP20447.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Johnston M., Nogae I.
    Submitted (DEC-1991) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "Sequence analysis of 203 kilobases from Saccharomyces cerevisiae chromosome VII."
    Rieger M., Brueckner M., Schaefer M., Mueller-Auer S.
    Yeast 13:1077-1090(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
    Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
    , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
    Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Identification of five putative yeast RNA helicase genes."
    Chang T.-H., Arenas J., Abelson J.
    Proc. Natl. Acad. Sci. U.S.A. 87:1571-1575(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 260-448.
  6. "Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required for efficient pre-rRNA processing predominantly at site A3."
    Weaver P.L., Sun C., Chang T.-H.
    Mol. Cell. Biol. 17:1354-1365(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  7. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiDBP3_YEAST
AccessioniPrimary (citable) accession number: P20447
Secondary accession number(s): D6VU66
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: October 1, 1996
Last modified: July 22, 2015
This is version 143 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 38900 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

External Data

Dasty 3

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 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.