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Protein

ATP-dependent RNA helicase DBP5

Gene

DBP5

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 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.11 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi138 – 145ATPPROSITE-ProRule annotation8

GO - Molecular functioni

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

GO - Biological processi

  • mRNA export from nucleus Source: SGD
  • protein transport Source: UniProtKB-KW
  • RNA secondary structure unwinding Source: GO_Central
  • translational termination Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

mRNA transport, Protein transport, Translocation, Transport

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33590-MONOMER.

Names & Taxonomyi

Protein namesi
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 namesi
Name:DBP5
Synonyms:RAT8
Ordered Locus Names:YOR046C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR046C.
SGDiS000005572. DBP5.

Subcellular locationi

GO - Cellular componenti

  • cellular bud tip Source: SGD
  • cytoplasm Source: SGD
  • nuclear membrane Source: UniProtKB-SubCell
  • nuclear pore Source: SGD
  • nuclear pore cytoplasmic filaments Source: SGD
  • nucleus Source: SGD
  • polysome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Membrane, Nuclear pore complex, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi170P → H in RAT8-7; accumulates poly(A)+ RNA in the nucleus at 16 degrees Celsius. 1 Publication1
Mutagenesisi171S → P in DBP5-2; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with L-236 and F-245. 1 Publication1
Mutagenesisi220L → P in DBP5-1; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with S-466. 1 Publication1
Mutagenesisi236F → L in DBP5-2; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with P-171 and F-245. 1 Publication1
Mutagenesisi267L → P in RAT8-2; accumulates poly(A)+ RNA in the nucleus at 16 and 37 degrees Celsius. 1 Publication1
Mutagenesisi345V → F in DBP5-2; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with P-171 and L-236. 1 Publication1
Mutagenesisi385I → D in RAT8-3; accumulates poly(A)+ RNA in the nucleus at 16 and 37 degrees Celsius. 1 Publication1
Mutagenesisi466T → S in DBP5-1; accumulates poly(A)+ RNA in the nucleus at 37 degrees Celsius; when associated with P-220. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000550191 – 482ATP-dependent RNA helicase DBP5Add BLAST482

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei86PhosphoserineCombined sources1
Modified residuei93PhosphoserineCombined sources1
Modified residuei162PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP20449.
PRIDEiP20449.

PTM databases

iPTMnetiP20449.

Interactioni

Subunit structurei

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 RAD3.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
GFD1Q048392EBI-5617,EBI-27549
ZDS1P501113EBI-5617,EBI-29626

Protein-protein interaction databases

BioGridi34447. 182 interactors.
DIPiDIP-2352N.
IntActiP20449. 7 interactors.
MINTiMINT-488024.

Structurei

Secondary structure

1482
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi78 – 80Combined sources3
Helixi83 – 85Combined sources3
Helixi87 – 90Combined sources4
Helixi94 – 97Combined sources4
Helixi101 – 109Combined sources9
Beta strandi110 – 113Combined sources4
Helixi117 – 127Combined sources11
Beta strandi128 – 130Combined sources3
Beta strandi134 – 137Combined sources4
Helixi144 – 155Combined sources12
Beta strandi165 – 168Combined sources4
Helixi172 – 185Combined sources14
Turni186 – 188Combined sources3
Beta strandi193 – 197Combined sources5
Beta strandi210 – 214Combined sources5
Helixi216 – 224Combined sources9
Beta strandi235 – 239Combined sources5
Helixi241 – 246Combined sources6
Helixi250 – 259Combined sources10
Turni261 – 264Combined sources4
Beta strandi266 – 272Combined sources7
Helixi276 – 285Combined sources10
Beta strandi290 – 292Combined sources3
Helixi296 – 298Combined sources3
Turni301 – 303Combined sources3
Beta strandi304 – 310Combined sources7
Helixi314 – 325Combined sources12
Turni326 – 329Combined sources4
Beta strandi330 – 336Combined sources7
Helixi340 – 352Combined sources13
Beta strandi358 – 360Combined sources3
Beta strandi362 – 364Combined sources3
Helixi366 – 377Combined sources12
Turni378 – 380Combined sources3
Beta strandi383 – 386Combined sources4
Helixi388 – 390Combined sources3
Beta strandi391 – 393Combined sources3
Beta strandi399 – 406Combined sources8
Beta strandi413 – 415Combined sources3
Helixi417 – 424Combined sources8
Helixi425 – 427Combined sources3
Beta strandi434 – 440Combined sources7
Helixi443 – 455Combined sources13
Turni456 – 458Combined sources3
Beta strandi462 – 465Combined sources4
Helixi469 – 480Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5ELXX-ray1.81A91-481[»]
ProteinModelPortaliP20449.
SMRiP20449.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP20449.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini125 – 292Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST168
Domaini303 – 480Helicase C-terminalPROSITE-ProRule annotationAdd BLAST178

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi92 – 120Q motifAdd BLAST29
Motifi239 – 242DEAD box4

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

GeneTreeiENSGT00530000063236.
HOGENOMiHOG000268797.
InParanoidiP20449.
KOiK18655.
OMAiFAPQANE.
OrthoDBiEOG092C2B1L.

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.

P20449-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDTKRDPAD LLASLKIDNE KEDTSEVSTK ETVKSQPEKT ADSIKPAEKL
60 70 80 90 100
VPKVEEKKTK QEDSNLISSE YEVKVKLADI QADPNSPLYS AKSFDELGLA
110 120 130 140 150
PELLKGIYAM KFQKPSKIQE RALPLLLHNP PRNMIAQSQS GTGKTAAFSL
160 170 180 190 200
TMLTRVNPED ASPQAICLAP SRELARQTLE VVQEMGKFTK ITSQLIVPDS
210 220 230 240 250
FEKNKQINAQ VIVGTPGTVL DLMRRKLMQL QKIKIFVLDE ADNMLDQQGL
260 270 280 290 300
GDQCIRVKRF LPKDTQLVLF SATFADAVRQ YAKKIVPNAN TLELQTNEVN
310 320 330 340 350
VDAIKQLYMD CKNEADKFDV LTELYGLMTI GSSIIFVATK KTANVLYGKL
360 370 380 390 400
KSEGHEVSIL HGDLQTQERD RLIDDFREGR SKVLITTNVL ARGIDIPTVS
410 420 430 440 450
MVVNYDLPTL ANGQADPATY IHRIGRTGRF GRKGVAISFV HDKNSFNILS
460 470 480
AIQKYFGDIE MTRVPTDDWD EVEKIVKKVL KD
Length:482
Mass (Da):53,874
Last modified:October 1, 1996 - v2
Checksum:iC50CAFE8C060D46B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28135 Genomic DNA. Translation: AAB01679.1.
Z74954 Genomic DNA. Translation: CAA99237.1.
Z74955 Genomic DNA. Translation: CAA99239.1.
BK006948 Genomic DNA. Translation: DAA10828.1.
PIRiS66920.
RefSeqiNP_014689.1. NM_001183465.1.

Genome annotation databases

EnsemblFungiiYOR046C; YOR046C; YOR046C.
GeneIDi854211.
KEGGisce:YOR046C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28135 Genomic DNA. Translation: AAB01679.1.
Z74954 Genomic DNA. Translation: CAA99237.1.
Z74955 Genomic DNA. Translation: CAA99239.1.
BK006948 Genomic DNA. Translation: DAA10828.1.
PIRiS66920.
RefSeqiNP_014689.1. NM_001183465.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5ELXX-ray1.81A91-481[»]
ProteinModelPortaliP20449.
SMRiP20449.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34447. 182 interactors.
DIPiDIP-2352N.
IntActiP20449. 7 interactors.
MINTiMINT-488024.

PTM databases

iPTMnetiP20449.

Proteomic databases

MaxQBiP20449.
PRIDEiP20449.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOR046C; YOR046C; YOR046C.
GeneIDi854211.
KEGGisce:YOR046C.

Organism-specific databases

EuPathDBiFungiDB:YOR046C.
SGDiS000005572. DBP5.

Phylogenomic databases

GeneTreeiENSGT00530000063236.
HOGENOMiHOG000268797.
InParanoidiP20449.
KOiK18655.
OMAiFAPQANE.
OrthoDBiEOG092C2B1L.

Enzyme and pathway databases

BioCyciYEAST:G3O-33590-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP20449.
PROiP20449.

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...

Entry informationi

Entry nameiDBP5_YEAST
AccessioniPrimary (citable) accession number: P20449
Secondary accession number(s): D6W2B2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: October 1, 1996
Last modified: November 2, 2016
This is version 172 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 14900 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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