P20447 (DBP3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ATP-dependent RNA helicase DBP3
EC=3.6.4.13

Alternative name(s):
DEAD box protein 3
Helicase CA3

Gene names

Name:	DBP3
Ordered Locus Names:	YGL078C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	523 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	ATP-dependent RNA helicase required for 60S ribosomal subunit synthesis. Involved in efficient pre-rRNA processing, predominantly at site A3, which is necessary for the normal formation of 25S and 5.8S rRNAs. Ref.6
Catalytic activity	ATP + H2O = ADP + phosphate.
Subcellular location	Nucleus › nucleolus Ref.6 Ref.7.
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 38900 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the DEAD box helicase family. DDX5/DBP2 subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.

Ontologies

Keywords
Biological process	Ribosome biogenesis rRNA processing
Cellular component	Nucleus
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Inferred from mutant phenotype Ref.6. Source: SGD
Cellular_component	nucleolus Inferred from direct assay Ref.6. Source: SGD preribosome, large subunit precursor Inferred from direct assay PubMed 22083961. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent RNA helicase activity Inferred from direct assay PubMed 23153376. 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 – 523	523	ATP-dependent RNA helicase DBP3		PRO_0000055017
Regions
	Domain	143 – 315	173	Helicase ATP-binding
	Domain	344 – 493	150	Helicase C-terminal
	Nucleotide binding	156 – 163	8	ATP By similarity
	Motif	114 – 140	27	Q motif
	Motif	262 – 265	4	DEAD box
Experimental info
	Sequence conflict	441	1	E → A no nucleotide entry Ref.5
	Sequence conflict	444	1	V → I no nucleotide entry Ref.5

Sequences

	Sequence		Length	Mass (Da)
	P20447 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: C198CF4E8D5BAFAA	FASTA	523	58,827
	10 20 30 40 50 60 MTKEEIADKK RKVVDEEVIE KKKSKKHKKD KKDKKEKKDK KHKKHKKEKK GEKEVEVPEK 70 80 90 100 110 120 ESEKKPEPTS AVASEFYVQS EALTSLPQSD IDEYFKENEI AVEDSLDLAL RPLLSFDYLS 130 140 150 160 170 180 LDSSIQAEIS KFPKPTPIQA VAWPYLLSGK DVVGVAETGS GKTFAFGVPA ISHLMNDQKK 190 200 210 220 230 240 RGIQVLVISP TRELASQIYD NLIVLTDKVG MQCCCVYGGV PKDEQRIQLK KSQVVVATPG 250 260 270 280 290 300 RLLDLLQEGS VDLSQVNYLV LDEADRMLEK GFEEDIKNII RETDASKRQT LMFTATWPKE 310 320 330 340 350 360 VRELASTFMN NPIKVSIGNT DQLTANKRIT QIVEVVDPRG KERKLLELLK KYHSGPKKNE 370 380 390 400 410 420 KVLIFALYKK EAARVERNLK YNGYNVAAIH GDLSQQQRTQ ALNEFKSGKS NLLLATDVAA 430 440 450 460 470 480 RGLDIPNVKT VINLTFPLTV EDYVHRIGRT GRAGQTGTAH TLFTEQEKHL AGGLVNVLNG 490 500 510 520 ANQPVPEDLI KFGTHTKKKE HSAYGSFFKD VDLTKKPKKI TFD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	Johnston M., Nogae I. Submitted (DEC-1991) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	"Sequence analysis of 203 kilobases from Saccharomyces cerevisiae chromosome VII." Rieger M., Brueckner M., Schaefer M., Mueller-Auer S. Yeast 13:1077-1090(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII." Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E. , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K. Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Identification of five putative yeast RNA helicase genes." Chang T.-H., Arenas J., Abelson J. Proc. Natl. Acad. Sci. U.S.A. 87:1571-1575(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 260-448.
[6]	"Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required for efficient pre-rRNA processing predominantly at site A3." Weaver P.L., Sun C., Chang T.-H. Mol. Cell. Biol. 17:1354-1365(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[7]	"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].
[8]	"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].
+	Additional computationally mapped references.

Web resources

RNA helicases from the baker's yeast Saccharomyces cerevisiae

Cross-references

Sequence databases
EMBL GenBank DDBJ	M80437 Genomic DNA. Translation: AAA73137.1. Z72600 Genomic DNA. Translation: CAA96783.1. BK006941 Genomic DNA. Translation: DAA08027.1.
PIR	S30805.
RefSeq	NP_011437.3. NM_001180943.3.
3D structure databases
ProteinModelPortal	P20447.
SMR	P20447. Positions 90-489.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2668N.
IntAct	P20447. 8 interactions.
MINT	MINT-1164200.
STRING	4932.YGL078C.
Proteomic databases
PaxDb	P20447.
PeptideAtlas	P20447.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YGL078C; YGL078C; YGL078C.
GeneID	852802.
KEGG	sce:YGL073W. sce:YGL078C.
Organism-specific databases
CYGD	YGL078c.
SGD	S000003046. DBP3.
Phylogenomic databases
eggNOG	COG0513.
GeneTree	ENSGT00680000100003.
HOGENOM	HOG000268804.
KO	K09419. K14811.
OMA	EEEWPEK.
OrthoDB	EOG42JS0S.
Gene expression databases
Genevestigator	P20447.
GermOnline	YGL078C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. IPR000629. RNA-helicase_DEAD-box_CS. IPR014014. RNA_helicase_DEAD_Q_motif. [Graphical view]
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	972321.

Entry information

Entry name

DBP3_YEAST

Accession

Primary (citable) accession number: P20447
Secondary accession number(s): D6VU66

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1991
Last sequence update:	October 1, 1996
Last modified:	May 1, 2013
This is version 123 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program