P25808 (SPB4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	606 AA.
Sequence status	Complete.
Protein existence	Evidence 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	Nucleus › nucleolus 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. Ref.7
Sequence similarities	Belongs to the DEAD box helicase family. DDX55/SPB4 subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.

Ontologies

Keywords
Biological process	Ribosome biogenesis rRNA processing
Cellular component	Nucleus
Domain	Coiled coil
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	rRNA processing Traceable author statement. Source: SGD ribosomal large subunit assembly Inferred from mutant phenotype. Source: SGD
Cellular component	90S preribosome Inferred from direct assay. Source: SGD nucleolus Traceable author statement. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent RNA helicase activity Traceable author statement. Source: SGD RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 606	606	ATP-dependent rRNA helicase SPB4		PRO_0000055065
Regions
	Domain	38 – 224	187	Helicase ATP-binding
	Domain	248 – 404	157	Helicase C-terminal
	Nucleotide binding	51 – 58	8	ATP By similarity
	Coiled coil	539 – 582	44	Potential
	Motif	7 – 35	29	Q motif
	Motif	172 – 175	4	DEAD box
Amino acid modifications
	Modified residue	254	1	Phosphoserine Ref.8

Sequences

	Sequence		Length	Mass (Da)
	P25808 [UniParc]. Last modified May 1, 1992. Version 1. Checksum: B2EC8B8B5E34AA10	FASTA	606	69,422
	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

References

	« Hide 'large scale' referencesShow '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: 2408148] [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: 8789262] [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: 7670463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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: 9769101] [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: 14562095] [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: 14562106] [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: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-254, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Web resources

RNA helicases from the baker's yeast Saccharomyces cerevisiae

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.
PIR	S14942.
RefSeq	NP_116654.1. NM_001179964.1.
3D structure databases
ProteinModelPortal	P25808.
SMR	P25808. Positions 14-377.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-5423N.
IntAct	P25808. 34 interactions.
MINT	MINT-525740.
STRING	P25808.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YFL002C; YFL002C; YFL002C.
GeneID	850549.
KEGG	sce:YFL002C.
NMPDR	fig|4932.3.peg.2285.
Organism-specific databases
CYGD	YFL002c.
SGD	S000001894. SPB4.
Phylogenomic databases
eggNOG	fuNOG05409.
GeneTree	EFGT00050000000140.
HOGENOM	HBG737336.
OMA	SANAELM.
OrthoDB	EOG46MFT3.
Gene expression databases
ArrayExpress	P25808.
Genevestigator	P25808.
GermOnline	YFL002C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR014001. DEAD-like_helicase. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR001650. Helicase_C. IPR000629. RNA-helicase_DEAD-box_CS. IPR014014. RNA_helicase_DEAD_Q_motif. [Graphical view]
KO	K14809.
Pfam	PF00270. DEAD. 1 hit. PF00271. Helicase_C. 1 hit. [Graphical view]
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
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
NextBio	966324.

Entry information

Entry name

SPB4_YEAST

Accession

Primary (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:	December 14, 2011
This is version 114 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program