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P20449 (DBP5_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 151. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
ATP-dependent RNA helicase DBP5

EC=3.6.4.13
Alternative name(s):
DEAD box protein 5
Helicase CA5/6
Ribonucleic acid-trafficking protein 8
Gene names
Name:DBP5
Synonyms:RAT8
Ordered Locus Names:YOR046C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length482 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. Contributes to the blocking of bulk poly(A)+ mRNA export in ethanol-stressed cells. May also be involved in early transcription. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.15 Ref.16 Ref.17

Catalytic activity

ATP + H2O = ADP + phosphate.

Subunit structure

Associates with the nuclear pore complex. Interacts with NUP159, GLE1, GFD1 and ZDS1. The interaction with NUP159 is necessary for the association to the nuclear pore complex. Interacts also with the TFIIH complex subunits TFB1, TFB2 and RAD3. Ref.7 Ref.8 Ref.9 Ref.12 Ref.16 Ref.17

Subcellular location

Cytoplasm. Nucleusnuclear pore complex. Nucleus membrane; Peripheral membrane protein; Cytoplasmic side. Note: Nuclear pore complex cytoplasmic fibrils. Accumulates in the nucleus rapidly and reversibly in response to ethanol stress. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.13 Ref.15 Ref.16

Domain

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

Miscellaneous

Present with 14900 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the DEAD box helicase family. DDX19/DBP5 subfamily.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Ontologies

Keywords
   Biological processmRNA transport
Protein transport
Translocation
Transport
   Cellular componentCytoplasm
Membrane
Nuclear pore complex
Nucleus
   LigandATP-binding
Nucleotide-binding
RNA-binding
   Molecular functionHelicase
Hydrolase
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processATP catabolic process

Inferred from direct assay PubMed 19805289. Source: GOC

mRNA export from nucleus

Inferred from mutant phenotype Ref.6. Source: SGD

protein transport

Inferred from electronic annotation. Source: UniProtKB-KW

translational termination

Inferred from genetic interaction PubMed 17272721. Source: SGD

   Cellular_componentcellular bud tip

Inferred from direct assay PubMed 19198597. Source: SGD

cytoplasm

Inferred from direct assay Ref.8Ref.15Ref.6. Source: SGD

nuclear membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

nuclear pore

Inferred from physical interaction Ref.7. Source: SGD

nuclear pore cytoplasmic filaments

Inferred from direct assay Ref.8. Source: SGD

nucleus

Inferred from direct assay Ref.15. Source: SGD

polysome

Inferred from direct assay PubMed 17272721. Source: SGD

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

ATP-dependent helicase activity

Inferred from electronic annotation. Source: InterPro

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA helicase activity

Inferred from direct assay Ref.5. Source: SGD

RNA-dependent ATPase activity

Inferred from direct assay PubMed 19805289. Source: SGD

protein binding

Inferred from physical interaction Ref.17. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

GFD1Q048392EBI-5617,EBI-27549
ZDS1P501113EBI-5617,EBI-29626

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 482482ATP-dependent RNA helicase DBP5
PRO_0000055019

Regions

Domain125 – 292168Helicase ATP-binding
Domain303 – 480178Helicase C-terminal
Nucleotide binding138 – 1458ATP By similarity
Motif92 – 12029Q motif
Motif239 – 2424DEAD box

Amino acid modifications

Modified residue861Phosphoserine Ref.18 Ref.19
Modified residue931Phosphoserine Ref.20
Modified residue1621Phosphoserine Ref.19

Experimental info

Mutagenesis1701P → H in RAT8-7; accumulates poly(A)+ RNA in the nucleus at 16 degrees Celsius. Ref.6
Mutagenesis1711S → P in DBP5-2; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with L-236 and F-245. Ref.5
Mutagenesis2201L → P in DBP5-1; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with S-466. Ref.5
Mutagenesis2361F → L in DBP5-2; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with P-171 and F-245. Ref.5
Mutagenesis2671L → P in RAT8-2; accumulates poly(A)+ RNA in the nucleus at 16 and 37 degrees Celsius. Ref.6
Mutagenesis3451V → F in DBP5-2; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with P-171 and L-236. Ref.5
Mutagenesis3851I → D in RAT8-3; accumulates poly(A)+ RNA in the nucleus at 16 and 37 degrees Celsius. Ref.6
Mutagenesis4661T → S in DBP5-1; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with P-220. Ref.5

Secondary structure

................................................................................... 482
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P20449 [UniParc].

Last modified October 1, 1996. Version 2.
Checksum: C50CAFE8C060D46B

FASTA48253,874
        10         20         30         40         50         60 
MSDTKRDPAD LLASLKIDNE KEDTSEVSTK ETVKSQPEKT ADSIKPAEKL VPKVEEKKTK 

        70         80         90        100        110        120 
QEDSNLISSE YEVKVKLADI QADPNSPLYS AKSFDELGLA PELLKGIYAM KFQKPSKIQE 

       130        140        150        160        170        180 
RALPLLLHNP PRNMIAQSQS GTGKTAAFSL TMLTRVNPED ASPQAICLAP SRELARQTLE 

       190        200        210        220        230        240 
VVQEMGKFTK ITSQLIVPDS FEKNKQINAQ VIVGTPGTVL DLMRRKLMQL QKIKIFVLDE 

       250        260        270        280        290        300 
ADNMLDQQGL GDQCIRVKRF LPKDTQLVLF SATFADAVRQ YAKKIVPNAN TLELQTNEVN 

       310        320        330        340        350        360 
VDAIKQLYMD CKNEADKFDV LTELYGLMTI GSSIIFVATK KTANVLYGKL KSEGHEVSIL 

       370        380        390        400        410        420 
HGDLQTQERD RLIDDFREGR SKVLITTNVL ARGIDIPTVS MVVNYDLPTL ANGQADPATY 

       430        440        450        460        470        480 
IHRIGRTGRF GRKGVAISFV HDKNSFNILS AIQKYFGDIE MTRVPTDDWD EVEKIVKKVL 


KD 

« Hide

References

« Hide 'large scale' references
[1]Chang T.-H.
Submitted (MAY-1995) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. expand/collapse author list , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"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 237-425.
[5]"Dbp5p, a cytosolic RNA helicase, is required for poly(A)+ RNA export."
Tseng S.S.-I., Weaver P.L., Liu Y., Hitomi M., Tartakoff A.M., Chang T.-H.
EMBO J. 17:2651-2662(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF SER-171; LEU-220; PHE-236; VAL-345 AND THR-466.
[6]"Dbp5p/Rat8p is a yeast nuclear pore-associated DEAD-box protein essential for RNA export."
Snay-Hodge C.A., Colot H.V., Goldstein A.L., Cole C.N.
EMBO J. 17:2663-2676(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF PRO-170; LEU-267 AND ILE-385.
[7]"Dbp5, a DEAD-box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p."
Schmitt C., von Kobbe C., Bachi A., Pante N., Rodrigues J.P., Boscheron C., Rigaut G., Wilm M., Seraphin B., Carmo-Fonseca M., Izaurralde E.
EMBO J. 18:4332-4347(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH NUP159, ASSOCIATION WITH THE NUCLEAR PORE COMPLEX, SUBCELLULAR LOCATION.
[8]"The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr255p."
Strahm Y., Fahrenkrog B., Zenklusen D., Rychner E., Kantor J., Rosbach M., Stutz F.
EMBO J. 18:5761-5777(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH GLE1, SUBCELLULAR LOCATION, ASSOCIATION WITH THE NUCLEAR PORE COMPLEX.
[9]"Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells."
Hodge C.A., Colot H.V., Stafford P., Cole C.N.
EMBO J. 18:5778-5788(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH NUP159 AND GLE1, ASSOCIATION WITH THE NUCLEAR PORE COMPLEX, SUBCELLULAR LOCATION.
[10]"Defects in the mRNA export factors Rat7p, Gle1p, Mex67p, and Rat8p cause hyperadenylation during 3'-end formation of nascent transcripts."
Hilleren P., Parker R.
RNA 7:753-764(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[11]"Coupling of termination, 3' processing, and mRNA export."
Hammell C.M., Gross S., Zenklusen D., Heath C.V., Stutz F., Moore C., Cole C.N.
Mol. Cell. Biol. 22:6441-6457(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[12]"An early function during transcription for the yeast mRNA export factor Dbp5p/Rat8p suggested by its genetic and physical interactions with transcription factor IIH components."
Estruch F., Cole C.N.
Mol. Biol. Cell 14:1664-1676(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH TFB1; TFB2 AND RAD3.
[13]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[14]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[15]"Stress response in yeast mRNA export factor: reversible changes in Rat8p localization are caused by ethanol stress but not heat shock."
Takemura R., Inoue Y., Izawa S.
J. Cell Sci. 117:4189-4197(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[16]"The N-terminal domain of Nup159 forms a beta-propeller that functions in mRNA export by tethering the helicase Dbp5 to the nuclear pore."
Weirich C.S., Erzberger J.P., Berger J.M., Weis K.
Mol. Cell 16:749-760(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH NUP159, SUBCELLULAR LOCATION.
[17]"Physical and genetic interactions link the yeast protein Zds1p with mRNA nuclear export."
Estruch F., Hodge C.A., Rodriguez-Navarro S., Cole C.N.
J. Biol. Chem. 280:9691-9697(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH GFD1 AND ZDS1.
[18]"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-86, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: ADR376.
[19]"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-86 AND SER-162, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[20]"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-93, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U28135 Genomic DNA. Translation: AAB01679.1.
Z74954 Genomic DNA. Translation: CAA99237.1.
Z74955 Genomic DNA. Translation: CAA99239.1.
BK006948 Genomic DNA. Translation: DAA10828.1.
PIRS66920.
RefSeqNP_014689.1. NM_001183465.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2KBENMR-A71-296[»]
2KBFNMR-A296-482[»]
3GFPX-ray1.80A296-482[»]
3PEUX-ray2.60A297-482[»]
3PEVX-ray2.50A297-482[»]
3PEWX-ray1.50A91-482[»]
3PEYX-ray1.40A91-482[»]
3RRMX-ray2.88A91-482[»]
3RRNX-ray4.00A91-482[»]
ProteinModelPortalP20449.
SMRP20449. Positions 71-481.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34447. 181 interactions.
DIPDIP-2352N.
IntActP20449. 7 interactions.
MINTMINT-488024.
STRING4932.YOR046C.

Proteomic databases

MaxQBP20449.
PaxDbP20449.
PeptideAtlasP20449.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOR046C; YOR046C; YOR046C.
GeneID854211.
KEGGsce:YOR046C.

Organism-specific databases

CYGDYOR046c.
SGDS000005572. DBP5.

Phylogenomic databases

eggNOGCOG0513.
GeneTreeENSGT00530000063236.
HOGENOMHOG000268797.
KOK01529.
OMADQCLRVK.
OrthoDBEOG7FNCJ0.

Enzyme and pathway databases

BioCycYEAST:G3O-33590-MONOMER.

Gene expression databases

GenevestigatorP20449.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
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]
PfamPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 1 hit.
PROSITEPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP20449.
NextBio976065.

Entry information

Entry nameDBP5_YEAST
AccessionPrimary (citable) accession number: P20449
Secondary accession number(s): D6W2B2
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: October 1, 1996
Last modified: June 11, 2014
This is version 151 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XV

Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references