P20449 (DBP5_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	482 AA.
Sequence status	Complete.
Protein existence	Evidence 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. Nucleus › nuclear 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 process	Protein transport Translocation Transport mRNA transport
Cellular component	Cytoplasm Membrane Nuclear pore complex Nucleus
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mRNA export from nucleus Inferred from genetic interaction Ref.6. Source: SGD protein transport Inferred from electronic annotation. Source: UniProtKB-KW translational termination Inferred from genetic interaction PubMed 17272721. Source: SGD
Cellular_component	cellular 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 cytoplasmic filaments Inferred from direct assay Ref.8. Source: SGD polysome Inferred from direct assay PubMed 17272721. Source: SGD
Molecular_function	ATP 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
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
GFD1	Q04839	2	EBI-5617,EBI-27549
ZDS1	P50111	3	EBI-5617,EBI-29626

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 482

482

ATP-dependent RNA helicase DBP5

PRO_0000055019

Regions

Domain

125 – 292

168

Helicase ATP-binding

Domain

303 – 480

178

Helicase C-terminal

Nucleotide binding

138 – 145

8

ATP By similarity

Motif

92 – 120

29

Q motif

Motif

239 – 242

4

DEAD box

Amino acid modifications

Modified residue

69

1

Phosphoserine Ref.19

Modified residue

86

1

Phosphoserine Ref.18 Ref.19

Modified residue

162

1

Phosphoserine Ref.19

Experimental info

Mutagenesis

170

1

P → H in RAT8-7; accumulates poly(A)+ RNA in the nucleus at 16 degrees Celsius. Ref.6

Mutagenesis

171

1

S → 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

Mutagenesis

220

1

L → P in DBP5-1; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with S-466. Ref.5

Mutagenesis

236

1

F → 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

Mutagenesis

267

1

L → P in RAT8-2; accumulates poly(A)+ RNA in the nucleus at 16 and 37 degrees Celsius. Ref.6

Mutagenesis

345

1

V → 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

Mutagenesis

385

1

I → D in RAT8-3; accumulates poly(A)+ RNA in the nucleus at 16 and 37 degrees Celsius. Ref.6

Mutagenesis

466

1

T → S in DBP5-1; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with P-220. Ref.5

Secondary structure

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482

Helix Strand Turn

Details...

Beta strand

78 – 80

3

Helix

83 – 85

3

Helix

87 – 90

4

Helix

94 – 97

4

Helix

101 – 109

9

Beta strand

110 – 113

4

Helix

117 – 127

11

Beta strand

128 – 130

3

Beta strand

134 – 137

4

Helix

144 – 155

12

Beta strand

165 – 168

4

Helix

172 – 185

14

Turn

186 – 188

3

Beta strand

193 – 197

5

Beta strand

210 – 214

5

Helix

216 – 224

9

Beta strand

235 – 239

5

Helix

241 – 246

6

Helix

250 – 259

10

Turn

261 – 264

4

Beta strand

266 – 272

7

Helix

276 – 285

10

Beta strand

290 – 292

3

Helix

296 – 298

3

Turn

301 – 303

3

Beta strand

304 – 310

7

Helix

314 – 325

12

Turn

326 – 329

4

Beta strand

330 – 336

7

Helix

340 – 352

13

Beta strand

358 – 360

3

Beta strand

362 – 364

3

Helix

366 – 377

12

Turn

378 – 380

3

Beta strand

383 – 386

4

Helix

388 – 390

3

Beta strand

391 – 393

3

Beta strand

399 – 406

8

Beta strand

413 – 415

3

Helix

417 – 424

8

Helix

425 – 427

3

Beta strand

434 – 440

7

Helix

443 – 455

13

Turn

456 – 458

3

Beta strand

462 – 465

4

Helix

469 – 480

12

Sequences

	Sequence		Length	Mass (Da)
	P20449 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: C50CAFE8C060D46B	FASTA	482	53,874
	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

References

	« Hide 'large scale' referencesShow '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. , 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 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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, MASS SPECTROMETRY. 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-69; SER-86 AND SER-162, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Web resources

RNA helicases from the baker's yeast Saccharomyces cerevisiae

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.

PIR

S66920.

RefSeq

NP_014689.1. NM_001183465.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2KBE	NMR	-	A	71-296	[»]
2KBF	NMR	-	A	296-482	[»]
3GFP	X-ray	1.80	A	296-482	[»]
3PEU	X-ray	2.60	A	297-482	[»]
3PEV	X-ray	2.50	A	297-482	[»]
3PEW	X-ray	1.50	A	91-482	[»]
3PEY	X-ray	1.40	A	91-482	[»]
3RRM	X-ray	2.88	A	91-482	[»]
3RRN	X-ray	4.00	A	91-482	[»]

ProteinModelPortal

P20449.

SMR

P20449. Positions 71-481.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2352N.

IntAct

P20449. 6 interactions.

MINT

MINT-488024.

STRING

4932.YOR046C.

Proteomic databases

PaxDb

P20449.

PeptideAtlas

P20449.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOR046C; YOR046C; YOR046C.

GeneID

854211.

KEGG

sce:YOR046C.

Organism-specific databases

CYGD

YOR046c.

SGD

S000005572. DBP5.

Phylogenomic databases

eggNOG

COG0513.

GeneTree

ENSGT00530000063236.

HOGENOM

HOG000268797.

KO

K01529.

OMA

PQAICLA.

OrthoDB

EOG4B2X5R.

Enzyme and pathway databases

BioCyc

YEAST:G3O-33590-MONOMER.

Gene expression databases

Genevestigator

P20449.

GermOnline

YOR046C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR011545. 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]

Pfam

PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]

SMART

SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]

SUPFAM

SSF52540. SSF52540. 1 hit.

PROSITE

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]

ProtoNet

Search...

Other

EvolutionaryTrace

P20449.

NextBio

976065.

Entry information

Entry name

DBP5_YEAST

Accession

Primary (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:	May 29, 2013
This is version 141 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program