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Protein

ATP-dependent RNA helicase DBP10

Gene

DBP10

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 the biogenesis of 60S ribosomal subunits and is required for the normal formation of 25S and 5.8S rRNAs.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi181 – 1888ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: SGD
  • identical protein binding Source: IntAct
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • assembly of large subunit precursor of preribosome Source: SGD
  • maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
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-29457-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DBP10 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 10
Gene namesi
Name:DBP10
Ordered Locus Names:YDL031W
ORF Names:D2770
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL031W.
SGDiS000002189. DBP10.

Subcellular locationi

GO - Cellular componenti

  • nucleolus Source: SGD
  • preribosome, large subunit precursor Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 995995ATP-dependent RNA helicase DBP10PRO_0000055040Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei101 – 1011PhosphoserineCombined sources
Modified residuei398 – 3981PhosphoserineCombined sources
Modified residuei400 – 4001PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ12389.
PeptideAtlasiQ12389.

PTM databases

iPTMnetiQ12389.

Interactioni

Subunit structurei

Interacts with RRP1 and associates with pre-ribosomal particles.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-5644,EBI-5644
DRS1P328924EBI-5644,EBI-6170
EBP2P360493EBI-5644,EBI-6289
HAS1Q035324EBI-5644,EBI-8170
LOC1P435865EBI-5644,EBI-22906
MAK21Q121763EBI-5644,EBI-10944
MAK5P381123EBI-5644,EBI-10394
NOC2P397445EBI-5644,EBI-29259
NOP4P378383EBI-5644,EBI-12122

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi32025. 59 interactions.
DIPiDIP-6387N.
IntActiQ12389. 31 interactions.
MINTiMINT-613064.

Structurei

3D structure databases

ProteinModelPortaliQ12389.
SMRiQ12389. Positions 138-579.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini168 – 340173Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini418 – 568151Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi137 – 16529Q motifAdd
BLAST
Motifi288 – 2914DEAD 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

GeneTreeiENSGT00550000075100.
HOGENOMiHOG000246455.
InParanoidiQ12389.
KOiK14808.
OMAiFPPQPKV.
OrthoDBiEOG7FR7R5.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR012541. DBP10_C.
IPR011545. 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]
PfamiPF08147. DBP10CT. 1 hit.
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
ProDomiPD024971. DBP10CT. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM01123. DBP10CT. 1 hit.
SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
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.

Q12389-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGVQKRKRD LEDQDDNGSE EDDIAFDIAN EIALNDSESD ANDSDSEVEA
60 70 80 90 100
DYGPNDVQDV IEYSSDEEEG VNNKKKAENK DIKKKKNSKK EIAAFPMLEM
110 120 130 140 150
SDDENNASGK TQTGDDEDDV NEYFSTNNLE KTKHKKGSFP SFGLSKIVLN
160 170 180 190 200
NIKRKGFRQP TPIQRKTIPL ILQSRDIVGM ARTGSGKTAA FILPMVEKLK
210 220 230 240 250
SHSGKIGARA VILSPSRELA MQTFNVFKDF ARGTELRSVL LTGGDSLEEQ
260 270 280 290 300
FGMMMTNPDV IIATPGRFLH LKVEMNLDLK SVEYVVFDEA DRLFEMGFQE
310 320 330 340 350
QLNELLASLP TTRQTLLFSA TLPNSLVDFV KAGLVNPVLV RLDAETKVSE
360 370 380 390 400
NLEMLFLSSK NADREANLLY ILQEIIKIPL ATSEQLQKLQ NSNNEADSDS
410 420 430 440 450
DDENDRQKKR RNFKKEKFRK QKMPAANELP SEKATILFVP TRHHVEYISQ
460 470 480 490 500
LLRDCGYLIS YIYGTLDQHA RKRQLYNFRA GLTSILVVTD VAARGVDIPM
510 520 530 540 550
LANVINYTLP GSSKIFVHRV GRTARAGNKG WAYSIVAENE LPYLLDLELF
560 570 580 590 600
LGKKILLTPM YDSLVDVMKK RWIDEGKPEY QFQPPKLSYT KRLVLGSCPR
610 620 630 640 650
LDVEGLGDLY KNLMSSNFDL QLAKKTAMKA EKLYYRTRTS ASPESLKRSK
660 670 680 690 700
EIISSGWDAQ NAFFGKNEEK EKLDFLAKLQ NRRNKETVFE FTRNPDDEMA
710 720 730 740 750
VFMKRRRKQL APIQRKATER RELLEKERMA GLSHSIEDEI LKGDDGETGY
760 770 780 790 800
TVSEDALKEF EDADQLLEAQ ENENKKKKKP KSFKDPTFFL SHYAPAGDIQ
810 820 830 840 850
DKQLQITNGF ANDAAQAAYD LNSDDKVQVH KQTATVKWDK KRKKYVNTQG
860 870 880 890 900
IDNKKYIIGE SGQKIAASFR SGRFDDWSKA RNLKPLKVGS RETSIPSNLL
910 920 930 940 950
EDPSQGPAAN GRTVRGKFKH KQMKAPKMPD KHRDNYYSQK KKVEKALQSG
960 970 980 990
ISVKGYNNAP GLRSELKSTE QIRKDRIIAE KKRAKNARPS KKRKF
Length:995
Mass (Da):112,946
Last modified:July 27, 2011 - v2
Checksum:i0533013C276095DF
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti733 – 7419SHSIEDEIL → HILSKMKFW in CAA96458 (PubMed:9046088).Curated
Sequence conflicti733 – 7419SHSIEDEIL → HILSKMKFW in CAA98590 (PubMed:9169867).Curated
Sequence conflicti746 – 7461G → V in CAA96458 (PubMed:9046088).Curated
Sequence conflicti746 – 7461G → V in CAA98590 (PubMed:9169867).Curated
Sequence conflicti764 – 7641D → H in CAA96458 (PubMed:9046088).Curated
Sequence conflicti764 – 7641D → H in CAA98590 (PubMed:9169867).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71781 Genomic DNA. Translation: CAA96458.1.
Z74079 Genomic DNA. Translation: CAA98590.1.
BK006938 Genomic DNA. Translation: DAA11821.2.
PIRiS67564.
RefSeqiNP_010253.2. NM_001180090.2.

Genome annotation databases

EnsemblFungiiYDL031W; YDL031W; YDL031W.
GeneIDi851530.
KEGGisce:YDL031W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71781 Genomic DNA. Translation: CAA96458.1.
Z74079 Genomic DNA. Translation: CAA98590.1.
BK006938 Genomic DNA. Translation: DAA11821.2.
PIRiS67564.
RefSeqiNP_010253.2. NM_001180090.2.

3D structure databases

ProteinModelPortaliQ12389.
SMRiQ12389. Positions 138-579.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32025. 59 interactions.
DIPiDIP-6387N.
IntActiQ12389. 31 interactions.
MINTiMINT-613064.

PTM databases

iPTMnetiQ12389.

Proteomic databases

MaxQBiQ12389.
PeptideAtlasiQ12389.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL031W; YDL031W; YDL031W.
GeneIDi851530.
KEGGisce:YDL031W.

Organism-specific databases

EuPathDBiFungiDB:YDL031W.
SGDiS000002189. DBP10.

Phylogenomic databases

GeneTreeiENSGT00550000075100.
HOGENOMiHOG000246455.
InParanoidiQ12389.
KOiK14808.
OMAiFPPQPKV.
OrthoDBiEOG7FR7R5.

Enzyme and pathway databases

BioCyciYEAST:G3O-29457-MONOMER.

Miscellaneous databases

PROiQ12389.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
InterProiIPR012541. DBP10_C.
IPR011545. 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]
PfamiPF08147. DBP10CT. 1 hit.
PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
ProDomiPD024971. DBP10CT. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM01123. DBP10CT. 1 hit.
SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
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. "The sequence of a 36.7 kb segment on the left arm of chromosome IV from Saccharomyces cerevisiae reveals 20 non-overlapping open reading frames (ORFs) including SIT4, FAD1, NAM1, RNA11, SIR2, NAT1, PRP9, ACT2 and MPS1 and 11 new ORFs."
    Saren A.-M., Laamanen P., Lejarcegui J.B., Paulin L.
    Yeast 13:65-71(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 733-741; 746 AND 764.
    Strain: ATCC 204508 / S288c.
  4. "Dbp10p, a putative RNA helicase from Saccharomyces cerevisiae, is required for ribosome biogenesis."
    Burger F., Daugeron M.-C., Linder P.
    Nucleic Acids Res. 28:2315-2323(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  5. "Role of the yeast Rrp1 protein in the dynamics of pre-ribosome maturation."
    Horsey E.W., Jakovljevic J., Miles T.D., Harnpicharnchai P., Woolford J.L. Jr.
    RNA 10:813-827(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RRP1, IDENTIFICATION BY MASS SPECTROMETRY.
  6. "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-101, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  7. "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-101; SER-398 AND SER-400, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "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-101, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiDBP10_YEAST
AccessioniPrimary (citable) accession number: Q12389
Secondary accession number(s): D6VRW1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 27, 2011
Last modified: June 8, 2016
This is version 152 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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 IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: 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.