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P25808 (SPB4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 135. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
ATP-dependent rRNA helicase SPB4

EC=3.6.4.-
Alternative name(s):
Suppressor of PAB1 protein 4
Gene names
Name:SPB4
Ordered Locus Names:YFL002C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length606 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits. Required for the normal formation of 18S rRNA through the processing of pre-rRNAs at sites A0, A1 and A2, and the normal formation of 25S and 5.8S rRNAs through the processing of pre-rRNAs at sites C1 and C2. Ref.1 Ref.5

Subcellular location

Nucleusnucleolus Ref.5 Ref.6.

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 5740 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the DEAD box helicase family. DDX55/SPB4 subfamily.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 606606ATP-dependent rRNA helicase SPB4
PRO_0000055065

Regions

Domain38 – 224187Helicase ATP-binding
Domain248 – 404157Helicase C-terminal
Nucleotide binding51 – 588ATP By similarity
Coiled coil539 – 58244 Potential
Motif7 – 3529Q motif
Motif172 – 1754DEAD box

Amino acid modifications

Modified residue2541Phosphoserine Ref.8

Sequences

Sequence LengthMass (Da)Tools
P25808 [UniParc].

Last modified May 1, 1992. Version 1.
Checksum: B2EC8B8B5E34AA10

FASTA60669,422
        10         20         30         40         50         60 
MSKSLEWDNL GFSLLPWIRT GLDVMGFETM TPVQASTIPM LAGNKDVVVD SVTGSGKTAA 

        70         80         90        100        110        120 
FVIPVLEKVV KEEANTSKFK KAHFHSLIIA PTRELSRQIE SVVLSFLEHY PSDLFPIKCQ 

       130        140        150        160        170        180 
LLVGTNEATV RDDVSNFLRN RPQILIGTPG RVLDFLQMPA VKTSACSMVV MDEADRLLDM 

       190        200        210        220        230        240 
SFIKDTEKIL RLLPKQRRTG LFSATMRSAG SDIFKTGLRN PVRITVNSKN QAPSSLKLNY 

       250        260        270        280        290        300 
CVVNPAEKLQ LLVSILNNYK FKKCIVYFPT CVSVSYFYSF IQYLGKRNIL VNEVEIFSLH 

       310        320        330        340        350        360 
GKLQTSARTK TLTAFTDSLS NSVLFTTDVA ARGIDIPDVD LVIQLDPPTN TDMFMHRCGR 

       370        380        390        400        410        420 
TGRANRVGKA ITFLNEGREE DFIPFMQVKN VELEELDLEV KGITTNFYED FRNWILEDRD 

       430        440        450        460        470        480 
RFDKGVKAYV AFIKYYSNHS ATSIFRLQSL DYVGIAKLYG LFRLPRMPEI TKYLATEKQE 

       490        500        510        520        530        540 
GIFPGNWLVD PPVNMDEYKY KDKKREKERQ ETLKNISLIN DKKKLKSELK KKNLAWSDKT 

       550        560        570        580        590        600 
LTKERKLERK EKMSLKRKAI EEELKAEELD ENAEEERIKE DWKEIVLQNK RKKVSSKAIQ 


GNFDDL 

« Hide

References

« Hide 'large scale' references
[1]"Translation initiation and ribosomal biogenesis: involvement of a putative rRNA helicase and RPL46."
Sachs A.B., Davis R.W.
Science 247:1077-1079(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]"Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI."
Naitou M., Ozawa M., Sasanuma S., Kobayashi M., Hagiwara H., Shibata T., Hanaoka F., Watanabe K., Ono A., Yamazaki M., Tashiro H., Eki T., Murakami Y.
Yeast 12:77-84(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204511 / S288c / AB972.
[3]"Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae."
Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S., Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H., Eki T.
Nat. Genet. 10:261-268(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]"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.
[5]"Spb4p, an essential putative RNA helicase, is required for a late step in the assembly of 60S ribosomal subunits in Saccharomyces cerevisiae."
de la Cruz J., Kressler D., Rojo M., Tollervey D., Linder P.
RNA 4:1268-1281(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[6]"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].
[7]"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].
[8]"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-254, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X16147 Genomic DNA. Translation: CAA34272.1.
D50617 Genomic DNA. Translation: BAA09238.1.
BK006940 Genomic DNA. Translation: DAA12439.1.
PIRS14942.
RefSeqNP_116654.1. NM_001179964.1.

3D structure databases

ProteinModelPortalP25808.
SMRP25808. Positions 18-429.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31147. 377 interactions.
DIPDIP-5423N.
IntActP25808. 34 interactions.
MINTMINT-525740.
STRING4932.YFL002C.

Proteomic databases

MaxQBP25808.
PaxDbP25808.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYFL002C; YFL002C; YFL002C.
GeneID850549.
KEGGsce:YFL002C.

Organism-specific databases

CYGDYFL002c.
SGDS000001894. SPB4.

Phylogenomic databases

eggNOGCOG0513.
GeneTreeENSGT00550000074969.
HOGENOMHOG000268803.
KOK14809.
OMAWDALTPP.
OrthoDBEOG7FR7R5.

Enzyme and pathway databases

BioCycYEAST:G3O-30452-MONOMER.

Gene expression databases

GenevestigatorP25808.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR025313. DUF4217.
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.
PF13959. DUF4217. 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

NextBio966324.
PROP25808.

Entry information

Entry nameSPB4_YEAST
AccessionPrimary (citable) accession number: P25808
Secondary accession number(s): D6VTM9
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: May 1, 1992
Last modified: June 11, 2014
This is version 135 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome VI

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

Yeast

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

SIMILARITY comments

Index of protein domains and families