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Protein

ATP-dependent RNA helicase DBP8

Gene

DBP8

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-binding RNA helicase involved in 40S ribosomal subunit biogenesis and is required for the normal formation of 18S rRNAs through pre-rRNA processing at A0, A1 and A2 sites. Required for vegetative growth.2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

pH dependencei

Optimum pH is 7.4.1 Publication

Temperature dependencei

Optimum temperature is 30 degrees Celsius.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi46 – 538ATP

GO - Molecular functioni

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

GO - Biological processi

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-31203-MONOMER.
ReactomeiR-SCE-6790901. rRNA modification in the nucleus.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DBP8 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 8
Gene namesi
Name:DBP8
Ordered Locus Names:YHR169W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VIII

Organism-specific databases

EuPathDBiFungiDB:YHR169W.
SGDiS000001212. DBP8.

Subcellular locationi

GO - Cellular componenti

  • nucleolus Source: SGD
  • nucleoplasm Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi51 – 522GK → AA in DBP8-1; loss of activity. 1 Publication
Mutagenesisi52 – 521K → A or R: Decreases ATPase activity in vitro. 1 Publication
Mutagenesisi155 – 1562DE → AA in DBP8-2; loss of activity. 1 Publication
Mutagenesisi155 – 1551D → A: Decreases ATPase activity in vitro. 1 Publication
Mutagenesisi188 – 1903TAT → AAA in DBP8-3; severely affects growth. 1 Publication
Mutagenesisi341 – 3422RS → AA in DBP8-4; no effect on growth. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 431431ATP-dependent RNA helicase DBP8PRO_0000055038Add
BLAST

Proteomic databases

MaxQBiP38719.

Interactioni

Subunit structurei

Interacts with ESF2.1 Publication

Protein-protein interaction databases

BioGridi36603. 60 interactions.
DIPiDIP-5628N.
IntActiP38719. 61 interactions.
MINTiMINT-485349.

Structurei

3D structure databases

ProteinModelPortaliP38719.
SMRiP38719. Positions 3-404.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini33 – 209177Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini242 – 389148Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi2 – 3029Q motifAdd
BLAST
Motifi155 – 1584DEAD 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

GeneTreeiENSGT00730000111231.
HOGENOMiHOG000268802.
InParanoidiP38719.
KOiK14778.
OMAiAKRESLM.
OrthoDBiEOG7FR7R5.

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.
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.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38719-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADFKSLGLS KWLTESLRAM KITQPTAIQK ACIPKILEGR DCIGGAKTGS
60 70 80 90 100
GKTIAFAGPM LTKWSEDPSG MFGVVLTPTR ELAMQIAEQF TALGSSMNIR
110 120 130 140 150
VSVIVGGESI VQQALDLQRK PHFIIATPGR LAHHIMSSGD DTVGGLMRAK
160 170 180 190 200
YLVLDEADIL LTSTFADHLA TCISALPPKD KRQTLLFTAT ITDQVKSLQN
210 220 230 240 250
APVQKGKPPL FAYQVESVDN VAIPSTLKIE YILVPEHVKE AYLYQLLTCE
260 270 280 290 300
EYENKTAIIF VNRTMTAEIL RRTLKQLEVR VASLHSQMPQ QERTNSLHRF
310 320 330 340 350
RANAARILIA TDVASRGLDI PTVELVVNYD IPSDPDVFIH RSGRTARAGR
360 370 380 390 400
IGDAISFVTQ RDVSRIQAIE DRINKKMTET NKVHDTAVIR KALTKVTKAK
410 420 430
RESLMAMQKE NFGERKRQQK KKQNDGKSLR S
Length:431
Mass (Da):47,878
Last modified:February 1, 1995 - v1
Checksum:iB0451EB85247372C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00027 Genomic DNA. Translation: AAB68014.1.
BK006934 Genomic DNA. Translation: DAA06862.1.
PIRiS48908.
RefSeqiNP_012039.1. NM_001179300.1.

Genome annotation databases

EnsemblFungiiYHR169W; YHR169W; YHR169W.
GeneIDi856574.
KEGGisce:YHR169W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00027 Genomic DNA. Translation: AAB68014.1.
BK006934 Genomic DNA. Translation: DAA06862.1.
PIRiS48908.
RefSeqiNP_012039.1. NM_001179300.1.

3D structure databases

ProteinModelPortaliP38719.
SMRiP38719. Positions 3-404.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36603. 60 interactions.
DIPiDIP-5628N.
IntActiP38719. 61 interactions.
MINTiMINT-485349.

Proteomic databases

MaxQBiP38719.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYHR169W; YHR169W; YHR169W.
GeneIDi856574.
KEGGisce:YHR169W.

Organism-specific databases

EuPathDBiFungiDB:YHR169W.
SGDiS000001212. DBP8.

Phylogenomic databases

GeneTreeiENSGT00730000111231.
HOGENOMiHOG000268802.
InParanoidiP38719.
KOiK14778.
OMAiAKRESLM.
OrthoDBiEOG7FR7R5.

Enzyme and pathway databases

BioCyciYEAST:G3O-31203-MONOMER.
ReactomeiR-SCE-6790901. rRNA modification in the nucleus.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus.

Miscellaneous databases

PROiP38719.

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.
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.
PROSITEiPS51192. 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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Characterization and mutational analysis of yeast Dbp8p, a putative RNA helicase involved in ribosome biogenesis."
    Daugeron M.-C., Linder P.
    Nucleic Acids Res. 29:1144-1155(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF 51-GLY-LYS-52; 155-ASP-GLU-156; 188-THR--THR-190 AND 341-ARG-SER-342.
  4. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis."
    Granneman S., Lin C., Champion E.A., Nandineni M.R., Zorca C., Baserga S.J.
    Nucleic Acids Res. 34:3189-3199(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION WITH ESF2, MUTAGENESIS OF LYS-52 AND ASP-155.

Entry informationi

Entry nameiDBP8_YEAST
AccessioniPrimary (citable) accession number: P38719
Secondary accession number(s): D3DLB8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: July 6, 2016
This is version 147 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 3500 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 VIII
    Yeast (Saccharomyces cerevisiae) chromosome VIII: 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.