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P20447

- DBP3_YEAST

UniProt

P20447 - DBP3_YEAST

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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: 5 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

  1. ATP binding Source: UniProtKB-KW
  2. ATP-dependent RNA helicase activity Source: SGD
  3. RNA binding Source: UniProtKB-KW
  4. RNA-dependent ATPase activity Source: SGD

GO - Biological processi

  1. ATP catabolic process Source: GOC
  2. endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
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: Chromosome VII

Organism-specific databases

CYGDiYGL078c.
SGDiS000003046. DBP3.

Subcellular locationi

Nucleusnucleolus 2 Publications

GO - Cellular componenti

  1. nucleolus Source: SGD
  2. 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.

Expressioni

Gene expression databases

GenevestigatoriP20447.

Interactioni

Protein-protein interaction databases

BioGridi33172. 116 interactions.
DIPiDIP-2668N.
IntActiP20447. 10 interactions.
MINTiMINT-1164200.
STRINGi4932.YGL078C.

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.
GeneTreeiENSGT00760000119744.
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:
EMBL
GenBank
DDBJ
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

Web resourcesi

RNA helicases from the baker's yeast Saccharomyces cerevisiae

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M80437 Genomic DNA. Translation: AAA73137.1 .
Z72600 Genomic DNA. Translation: CAA96783.1 .
BK006941 Genomic DNA. Translation: DAA08027.1 .
PIRi S30805.
RefSeqi NP_011437.3. NM_001180943.3.

3D structure databases

ProteinModelPortali P20447.
SMRi P20447. Positions 90-489.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 33172. 116 interactions.
DIPi DIP-2668N.
IntActi P20447. 10 interactions.
MINTi MINT-1164200.
STRINGi 4932.YGL078C.

Proteomic databases

MaxQBi P20447.
PaxDbi P20447.
PeptideAtlasi P20447.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YGL078C ; YGL078C ; YGL078C .
GeneIDi 852802.
KEGGi sce:YGL078C.

Organism-specific databases

CYGDi YGL078c.
SGDi S000003046. DBP3.

Phylogenomic databases

eggNOGi COG0513.
GeneTreei ENSGT00760000119744.
HOGENOMi HOG000268804.
InParanoidi P20447.
KOi K14811.
OMAi PIQSASW.
OrthoDBi EOG7TJ3T2.

Enzyme and pathway databases

BioCyci YEAST:G3O-30579-MONOMER.

Miscellaneous databases

NextBioi 972321.

Gene expression databases

Genevestigatori P20447.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR011545. 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 ]
Pfami PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view ]
SMARTi SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 1 hit.
PROSITEi PS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: October 29, 2014
This is version 136 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