P38712 (RRP3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ATP-dependent rRNA helicase RRP3
EC=3.6.4.-

Alternative name(s):
Ribosomal RNA-processing protein 3

Gene names

Name:	RRP3
Ordered Locus Names:	YHR065C

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	501 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required for pre-ribosomal RNA processing. Involved in the maturation of the 35S-pre-rRNA and to its cleavage to mature 18S rRNA. Ref.4
Subcellular location	Nucleus Probable.
Domain	The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.
Sequence similarities	Belongs to the DEAD box helicase family. DDX47/RRP3 subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.
Sequence caution	The sequence AAB68392.1 differs from that shown. Reason: Erroneous initiation.

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	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Inferred from mutant phenotype PubMed 16449634. Source: SGD
Cellular_component	nucleolus Inferred by curator PubMed 16449634. 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 – 501	501	ATP-dependent rRNA helicase RRP3		PRO_0000055064
Regions
	Domain	112 – 284	173	Helicase ATP-binding
	Domain	307 – 461	155	Helicase C-terminal
	Nucleotide binding	125 – 132	8	ATP By similarity
	Coiled coil	3 – 44	42	Potential
	Motif	81 – 109	29	Q motif
	Motif	231 – 234	4	DEAD box
Amino acid modifications
	Modified residue	43	1	Phosphoserine Ref.6 Ref.7
	Modified residue	45	1	Phosphoserine Ref.6 Ref.7
	Modified residue	47	1	Phosphoserine Ref.6 Ref.7

Sequences

	Sequence		Length	Mass (Da)
	P38712 [UniParc]. Last modified November 8, 2005. Version 2. Checksum: AA17798E0897272F	FASTA	501	55,969
	10 20 30 40 50 60 MSKIVKRKEK KANDELTSLA EKIRAKALEN QKKLIEAEKE GGSESDSEED ATAEKKKVLK 70 80 90 100 110 120 SKSKSTVSTQ NENTNEDESF ESFSELNLVP ELIQACKNLN YSKPTPIQSK AIPPALEGHD 130 140 150 160 170 180 IIGLAQTGSG KTAAFAIPIL NRLWHDQEPY YACILAPTRE LAQQIKETFD SLGSLMGVRS 190 200 210 220 230 240 TCIVGGMNMM DQARDLMRKP HIIIATPGRL MDHLENTKGF SLRKLKFLVM DEADRLLDME 250 260 270 280 290 300 FGPVLDRILK IIPTQERTTY LFSATMTSKI DKLQRASLTN PVKCAVSNKY QTVDTLVQTL 310 320 330 340 350 360 MVVPGGLKNT YLIYLLNEFI GKTMIIFTRT KANAERLSGL CNLLEFSATA LHGDLNQNQR 370 380 390 400 410 420 MGSLDLFKAG KRSILVATDV AARGLDIPSV DIVVNYDIPV DSKSYIHRVG RTARAGRSGK 430 440 450 460 470 480 SISLVSQYDL ELILRIEEVL GKKLPKESVD KNIILTLRDS VDKANGEVVM EMNRRNKEKI 490 500 ARGKGRRGRM MTRENMDMGE R

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M. Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"Verification of 3' and 5' ends of S.cerevisiae transcripts." Kennedy M.C., Dietrich F.S. Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-72 AND 478-501. Strain: ATCC 204511 / S288c / AB972.
[4]	"18S rRNA processing requires the RNA helicase-like protein Rrp3." O'Day C.L., Chavanikamannil F., Abelson J. Nucleic Acids Res. 24:3201-3207(1996) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[5]	"Sequencing and comparison of yeast species to identify genes and regulatory elements." Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S. Nature 423:241-254(2003) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
[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-43; SER-45 AND SER-47, MASS SPECTROMETRY. 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-43; SER-45 AND SER-47, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Web resources

RNA helicases from the baker's yeast Saccharomyces cerevisiae

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00061 Genomic DNA. Translation: AAB68392.1. Different initiation. AY389302 mRNA. Translation: AAQ97234.1. AY389303 mRNA. Translation: AAQ97235.1. BK006934 Genomic DNA. Translation: DAA06758.1.
PIR	S46713.
RefSeq	NP_011932.2. NM_001179195.1.
3D structure databases
ProteinModelPortal	P38712.
SMR	P38712. Positions 76-446.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-6533N.
IntAct	P38712. 1 interaction.
MINT	MINT-518716.
Proteomic databases
PaxDb	P38712.
PeptideAtlas	P38712.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YHR065C; YHR065C; YHR065C.
GeneID	856462.
KEGG	sce:YHR065C.
Organism-specific databases
CYGD	YHR065c.
SGD	S000001107. RRP3.
Phylogenomic databases
eggNOG	COG0513.
GeneTree	ENSGT00670000098028.
HOGENOM	HOG000268802.
KO	K14777.
OMA	IFIPSKF.
OrthoDB	EOG4ZPJ3P.
Gene expression databases
Genevestigator	P38712.
GermOnline	YHR065C. 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	982111.

Entry information

Entry name

RRP3_YEAST

Accession

Primary (citable) accession number: P38712
Secondary accession number(s): D3DL14, Q6TQT5, Q6TQT6

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	November 8, 2005
Last modified:	May 1, 2013
This is version 115 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program