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Protein

ATP-dependent RNA helicase DBP2

Gene

DBP2

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 RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi157 – 1648ATP

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

  • messenger ribonucleoprotein complex assembly Source: SGD
  • nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: SGD
  • rRNA processing Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Nonsense-mediated mRNA decay, Ribosome biogenesis, rRNA processing

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33136-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DBP2 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 2
p68-like protein
Gene namesi
Name:DBP2
Ordered Locus Names:YNL112W
ORF Names:N1945
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL112W.
SGDiS000005056. DBP2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi163 – 1631K → R: Decreases nonsense-mediated mRNA decay. 1 Publication
Mutagenesisi268 – 2681E → D: Decreases nonsense-mediated mRNA decay. 1 Publication
Mutagenesisi300 – 3001T → A: Decreases nonsense-mediated mRNA decay. 1 Publication
Mutagenesisi447 – 4471R → K: Decreases nonsense-mediated mRNA decay. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 546546ATP-dependent RNA helicase DBP2PRO_0000055000Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei88 – 881PhosphoserineCombined sources
Modified residuei90 – 901PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP24783.
PeptideAtlasiP24783.

PTM databases

iPTMnetiP24783.

Interactioni

Subunit structurei

Interacts with UPF1. Associates with polysomes.2 Publications

Protein-protein interaction databases

BioGridi35713. 74 interactions.
DIPiDIP-2438N.
IntActiP24783. 41 interactions.
MINTiMINT-636962.

Structurei

3D structure databases

ProteinModelPortaliP24783.
SMRiP24783. Positions 62-490.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini144 – 319176Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini347 – 494148Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni505 – 53026RNA-binding RGG-boxAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi113 – 14129Q motifAdd
BLAST
Motifi267 – 2704DEAD 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

GeneTreeiENSGT00820000126976.
HOGENOMiHOG000268804.
InParanoidiP24783.
KOiK12823.
OMAiVKFHEAA.
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.

P24783-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTYGGRDQQY NKTNYKSRGG DFRGGRNSDR NSYNDRPQGG NYRGGFGGRS
60 70 80 90 100
NYNQPQELIK PNWDEELPKL PTFEKNFYVE HESVRDRSDS EIAQFRKENE
110 120 130 140 150
MTISGHDIPK PITTFDEAGF PDYVLNEVKA EGFDKPTGIQ CQGWPMALSG
160 170 180 190 200
RDMVGIAATG SGKTLSYCLP GIVHINAQPL LAPGDGPIVL VLAPTRELAV
210 220 230 240 250
QIQTECSKFG HSSRIRNTCV YGGVPKSQQI RDLSRGSEIV IATPGRLIDM
260 270 280 290 300
LEIGKTNLKR VTYLVLDEAD RMLDMGFEPQ IRKIVDQIRP DRQTLMWSAT
310 320 330 340 350
WPKEVKQLAA DYLNDPIQVQ VGSLELSASH NITQIVEVVS DFEKRDRLNK
360 370 380 390 400
YLETASQDNE YKTLIFASTK RMCDDITKYL REDGWPALAI HGDKDQRERD
410 420 430 440 450
WVLQEFRNGR SPIMVATDVA ARGIDVKGIN YVINYDMPGN IEDYVHRIGR
460 470 480 490 500
TGRAGATGTA ISFFTEQNKG LGAKLISIMR EANQNIPPEL LKYDRRSYGG
510 520 530 540
GHPRYGGGRG GRGGYGRRGG YGGGRGGYGG NRQRDGGWGN RGRSNY
Length:546
Mass (Da):60,999
Last modified:March 1, 1992 - v1
Checksum:i30FE3D4C7E653120
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti425 – 4251D → GN in CAA93395 (PubMed:9090055).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X52649 Genomic DNA. Translation: CAA36874.1.
Z71388 Genomic DNA. Translation: CAA95991.1.
Z69382 Genomic DNA. Translation: CAA93395.1.
M64991 Genomic DNA. No translation available.
BK006947 Genomic DNA. Translation: DAA10435.1.
PIRiS13757.
RefSeqiNP_014287.3. NM_001182950.3.

Genome annotation databases

EnsemblFungiiYNL112W; YNL112W; YNL112W.
GeneIDi855611.
KEGGisce:YNL112W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X52649 Genomic DNA. Translation: CAA36874.1.
Z71388 Genomic DNA. Translation: CAA95991.1.
Z69382 Genomic DNA. Translation: CAA93395.1.
M64991 Genomic DNA. No translation available.
BK006947 Genomic DNA. Translation: DAA10435.1.
PIRiS13757.
RefSeqiNP_014287.3. NM_001182950.3.

3D structure databases

ProteinModelPortaliP24783.
SMRiP24783. Positions 62-490.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35713. 74 interactions.
DIPiDIP-2438N.
IntActiP24783. 41 interactions.
MINTiMINT-636962.

PTM databases

iPTMnetiP24783.

Proteomic databases

MaxQBiP24783.
PeptideAtlasiP24783.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL112W; YNL112W; YNL112W.
GeneIDi855611.
KEGGisce:YNL112W.

Organism-specific databases

EuPathDBiFungiDB:YNL112W.
SGDiS000005056. DBP2.

Phylogenomic databases

GeneTreeiENSGT00820000126976.
HOGENOMiHOG000268804.
InParanoidiP24783.
KOiK12823.
OMAiVKFHEAA.
OrthoDBiEOG7TJ3T2.

Enzyme and pathway databases

BioCyciYEAST:G3O-33136-MONOMER.

Miscellaneous databases

PROiP24783.

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. "p68 RNA helicase: identification of a nucleolar form and cloning of related genes containing a conserved intron in yeasts."
    Iggo R.D., Jamieson D.J., McNeill S.A., Southgate J., McPheat J., Lane D.P.
    Mol. Cell. Biol. 11:1326-1333(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The DNA sequence of cosmid 14-13b from chromosome XIV of Saccharomyces cerevisiae reveals an unusually high number of overlapping open reading frames."
    de Antoni A., D'Angelo M., Dal Pero F., Sartorello F., Pandolfo D., Pallavicini A., Lanfranchi G., Valle G.
    Yeast 13:261-266(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
    Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
    , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
    Nature 387:93-98(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. "RPC19, the gene for a subunit common to yeast RNA polymerases A (I) and C (III)."
    Dequard-Chablat M., Riva M., Carles C., Sentenac A.
    J. Biol. Chem. 266:15300-15307(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-18.
  6. "Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen."
    He F., Jacobson A.
    Genes Dev. 9:437-454(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH UPF1.
  7. "Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing."
    Bond A.T., Mangus D.A., He F., Jacobson A.
    Mol. Cell. Biol. 21:7366-7379(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH UPF1, MUTAGENESIS OF LYS-163; GLU-268; THR-300 AND ARG-447.
  8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-90, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  11. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
    Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
    Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-88 AND SER-90, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-88 AND SER-90, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
    Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
    Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiDBP2_YEAST
AccessioniPrimary (citable) accession number: P24783
Secondary accession number(s): D6W169, Q05456
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: March 1, 1992
Last modified: June 8, 2016
This is version 167 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 33100 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: 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.