Protein Overview: RRP3

General Information:
Name(s) found:	RRP3 / YHR065C [SGD]
Description(s) found: SHOW ONLY BEST	gi\|81175193\|sp\|P38712.2\|RRP3_YEAST RecName: Full=ATP-dependent rRNA helicase RRP3; AltName: Full=Ribosomal RNA-processing protein 3 [NCBI NR] gi\|37362659\|ref\|NP_011932.2\| Protein involved in rRNA processing; required for maturation of the 35S primary transcript of pre-rRNA and for cleavage leading to mature 18S rRNA; homologous to eIF-4a, which is a DEAD box RNA-dependent ATPase with helicase a [NCBI NR] ATP-dependent rRNA helicase RRP3 OS=Saccharomyces cerevisiae GN=RRP3 PE=1 SV=2 [Swiss-Prot] RRP3 Protein required for maturation of the 35S primary transcript [mips] Protein involved in rRNA processing; required for maturation of the 35S primary transcript of pre-rRNA and for cleavage leading to mature 18S rRNA; homologous to eIF-4a, which is a DEAD box RNA-dependent ATPase with helicase activity [SGD] Chr VIII from 229038-227533, reverse complement [yeastorf5.fasta] RRP3 SGDID:S0001107, Chr VIII from 229038-227533, reverse complement, Verified ORF [yeastflysequest.fasta] Required for maturation of the 35S primary transcript of pre-rRNA and is required for cleavages leading to mature 18S RNA; RRP3 is a DEAD box gene homologous to eIF-4a which encodes an RNA-dependent ATPase possessing helicase activity which is not specifi [nrdb_11152004_Chlamydomonas] RRP3 SGDID:S000001107, Chr VIII from 229039-227534, reverse complement, Verified ORF, "Protein involved in rRNA processing; required for maturation of the 35S primary transcript of pre-rRNA and for cleavage leading to mature 18S rRNA; homologous to eIF-4a [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] ATP-dependent rRNA helicase RRP3 (Ribosomal RNA-processing protein RRP3) [nr-271106-contam.fasta] Protein involved in rRNA processing; required for maturation of the 35S primary transcript of pre-rRNA and for cleavage leading to mature 18S rRNA; homologous to eIF-4a, which is a DEAD box RNA-dependent ATPase with helicase activity; Rrp3p [Saccharomyces [nr-271106-contam.fasta] RRP3 SGDID:S000001107, Chr VIII from 229039-227534, reverse complement, Verified ORF, "Protein involved in rRNA processing; required for maturation of the 35S primary transcript of pre-rRNA and for cleavage leading to mature 18S rRNA; homologous to eIF-4a, which is a DEAD box RNA-dependent ATPase with helicase activity" [yeast-bovrabprots.fasta] [chemostatdb.fasta] ATP-dependent rRNA helicase RRP3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RRP3 PE=1 SV=2 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta] RRP3 SGDID:S000001107, Chr VIII from 229037-227532, Genome Release 64-1-1, reverse complement, Verified ORF, "Protein involved in rRNA processing; required for maturation of the 35S primary transcript of pre-rRNA and for cleavage leading to mature 18S rRNA; homologous to eIF-4a, which is a DEAD box RNA-dependent ATPase with helicase activity" [yeast-030211-contam.fasta] RRP3 SGDID:S000001107, Chr VIII from 229037-227532, Genome Release 64-2-1, reverse complement, Verified ORF, "Protein involved in rRNA processing; required for maturation of the 35S primary transcript of pre-rRNA and for cleavage leading to mature 18S rRNA; homologous to eIF-4a, which is a DEAD box RNA-dependent ATPase with helicase activity" [20141208_orf_trans.fasta] YHR065C SGDID:S000001107, Chr VIII from 229037-227532, Genome Release 64-1-1, reverse complement, Verified ORF, "Protein involved in rRNA processing; required for maturation of the 35S primary transcript of pre-rRNA and for cleavage leading to mature 18S rRNA; homologous to eIF-4a, which is a DEAD box RNA-dependent ATPase with helicase activity" [2016-01-SGD_Yeast_Contam_Riffle_20140507-Ska-Hec-110-tubulin.fasta]
Organism:	Saccharomyces cerevisiae
Length:	501 amino acids
Gene Ontology:
Cellular Component:	nuclear outer membrane [TAS] nucleolus [TAS]
Biological Process:	ribosome biogenesis [RCA]
Molecular Function:	ATP-dependent RNA helicase activity [TAS]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSKIVKRKEK KANDELTSLA EKIRAKALEN QKKLIEAEKE GGSESDSEED ATAEKKKVLK  60
   61 SKSKSTVSTQ NENTNEDESF ESFSELNLVP ELIQACKNLN YSKPTPIQSK AIPPALEGHD 120
  121 IIGLAQTGSG KTAAFAIPIL NRLWHDQEPY YACILAPTRE LAQQIKETFD SLGSLMGVRS 180
  181 TCIVGGMNMM DQARDLMRKP HIIIATPGRL MDHLENTKGF SLRKLKFLVM DEADRLLDME 240
  241 FGPVLDRILK IIPTQERTTY LFSATMTSKI DKLQRASLTN PVKCAVSNKY QTVDTLVQTL 300
  301 MVVPGGLKNT YLIYLLNEFI GKTMIIFTRT KANAERLSGL CNLLEFSATA LHGDLNQNQR 360
  361 MGSLDLFKAG KRSILVATDV AARGLDIPSV DIVVNYDIPV DSKSYIHRVG RTARAGRSGK 420
  421 SISLVSQYDL ELILRIEEVL GKKLPKESVD KNIILTLRDS VDKANGEVVM EMNRRNKEKI 480
  481 ARGKGRRGRM MTRENMDMGE R

Protein Complex Data

	PUBLICATION	TOPOLOGY	COCOMPLEXED PROTEINS
View Details	Riffle et al. (2010) (Unpublished Data)		ESF1 ESF2 HCA4 RPS11A, RPS11B RRP3
View Details	(MIPS) Mewes HW, et al. (2004)		DRS1 GAR1 IFH1 NOP1 NPL3 NSR1 POP1 POP2 RAT1 RNT1 RRP3 SBP1 SNM1 SRD1 UTP10 UTP11 UTP13 UTP4 UTP5 UTP6 UTP7 UTP8 UTP9 YME2
View Details	Krogan NJ, et al. (2006)		ENP2 ESF1 PUT3 RRP3
View Details	Ho Y, et al. (2002)		ACC1 ADR1 ATP3 CCT3 COP1 CPA2 DEF1 FOL2 GAL7 IDH1 LSC1 LST8 LYS12 PHO86 POR1 RPN12 RRP3 SIP1 SLC1 STI1 YBT1 YKU80 YML020W
View Details	Qiu et al. (2008)		AIR1 DBP10 DBP3 DBP6 DBP7 DBP9 DHR2 DIP2 DRS1 GAR1 HAS1 HCA4 MAK5 MPP10 MRD1 MTR4 NOP15 NSR1 NUG1 POP1 RNT1 ROK1 RRP3 RRP5 RRP9 SOF1 SPB4 UTP13 UTP9

Mass Spectrometry Data

The following runs contain data for this protein:

	BAIT	COMMENTS	PUBLICATION
View Run	RPA135	No Comments	Schneider, DA, et al. (2006)
View Run	MLP2	#31 Asynchronous Prep (Protease cleavage)	Keck JM, et al. (2011)

Yeast Two-Hybrid Data

The following interactions contain this protein:

SHOWING SINGLE HITS. [ Hide Single Hits ]

[View our yeast two-hybrid interpretation guidelines.]

	BAIT	PREY	HITS	PUBLICATION
View Screen	GPA1	RRP3	1	Unpublished Fields Lab Data
View Screen	SPT23	RRP3	1	Unpublished Fields Lab Data
View Screen	RPB2	RRP3	1	Unpublished Fields Lab Data

Microscopy / Localization Data

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No microscopy data found in the PDR for this protein.

Protein Structure Data

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[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..501]	PSI-BLAST	56.154902	Initiation factor 4a

Functions predicted (by domain):

Gene Ontology predictions

Term	Confidence	Notes
translation initiation factor activity	7.79457008386475	bayes_pls_golite062009
translation factor activity, nucleic acid binding	4.98637553020315	bayes_pls_golite062009
translation regulator activity	4.94658029227343	bayes_pls_golite062009
	4.704140727858	bayes_pls_golite062009
structural constituent of ribosome	4.56509805974548	bayes_pls_golite062009
structural molecule activity	3.58406348799895	bayes_pls_golite062009
DNA clamp loader activity	3.22518920754305	bayes_pls_golite062009
protein-DNA loading ATPase activity	3.19273435123154	bayes_pls_golite062009
nucleoside-triphosphatase activity	2.95079405147356	bayes_pls_golite062009
pyrophosphatase activity	2.87427509025394	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	2.85499564954033	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	2.85178667290149	bayes_pls_golite062009
motor activity	2.79327761685782	bayes_pls_golite062009
microtubule motor activity	2.74365461017633	bayes_pls_golite062009
DNA-dependent ATPase activity	2.72462789867829	bayes_pls_golite062009
binding	2.64537357529343	bayes_pls_golite062009
transporter activity	2.58140740499725	bayes_pls_golite062009
hydrolase activity	2.55157966585974	bayes_pls_golite062009
nucleic acid binding	2.51683451033161	bayes_pls_golite062009
transmembrane transporter activity	2.39695871109024	bayes_pls_golite062009
ATPase activity	2.39535714892224	bayes_pls_golite062009
RNA binding	2.29590582680214	bayes_pls_golite062009
DNA helicase activity	2.2817164193758	bayes_pls_golite062009
ATPase activity, coupled	2.18396165590908	bayes_pls_golite062009
RNA cap binding	2.17871969124431	bayes_pls_golite062009
DNA binding	2.12258000781149	bayes_pls_golite062009
transcription regulator activity	2.09345198747025	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.88455339138556	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
RNA helicase activity	1.42791449104435	bayes_pls_golite062009
cytoskeletal protein binding	1.40488517180956	bayes_pls_golite062009
RNA-dependent ATPase activity	1.39335733374328	bayes_pls_golite062009
ATP-dependent RNA helicase activity	1.36724390116598	bayes_pls_golite062009
DNA strand annealing activity	1.30936388901516	bayes_pls_golite062009
substrate-specific transporter activity	1.29730375126024	bayes_pls_golite062009
telomeric DNA binding	1.28350783207533	bayes_pls_golite062009
structure-specific DNA binding	1.2539059700735	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
double-stranded DNA binding	1.117585097627	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
tubulin binding	0.979946830272106	bayes_pls_golite062009
DNA-directed DNA polymerase activity	0.971476020912368	bayes_pls_golite062009
purine nucleotide binding	0.929901285538132	bayes_pls_golite062009
DNA polymerase activity	0.928091843881235	bayes_pls_golite062009
nucleotide binding	0.922442819194247	bayes_pls_golite062009
purine ribonucleotide binding	0.920987930180051	bayes_pls_golite062009
ribonucleotide binding	0.920926158369519	bayes_pls_golite062009
microtubule binding	0.907162506177187	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	0.906554174337376	bayes_pls_golite062009
transcription factor activity	0.887108427603557	bayes_pls_golite062009
actin binding	0.883285269827407	bayes_pls_golite062009
transcription repressor activity	0.862685397469217	bayes_pls_golite062009
mRNA binding	0.76699944561918	bayes_pls_golite062009
transcription elongation regulator activity	0.752795599437554	bayes_pls_golite062009
ribonuclease activity	0.712344060953362	bayes_pls_golite062009
single-stranded DNA binding	0.568457189190858	bayes_pls_golite062009
GTPase activity	0.437665353870877	bayes_pls_golite062009
active transmembrane transporter activity	0.434775387083003	bayes_pls_golite062009
snRNA binding	0.418985924846052	bayes_pls_golite062009
ATP binding	0.41092997612902	bayes_pls_golite062009
adenyl ribonucleotide binding	0.385813421701492	bayes_pls_golite062009
adenyl nucleotide binding	0.377870145186619	bayes_pls_golite062009
ion transmembrane transporter activity	0.355466224802969	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	0.328170855722634	bayes_pls_golite062009
mismatched DNA binding	0.31144582840038	bayes_pls_golite062009
guanyl nucleotide binding	0.296406132096546	bayes_pls_golite062009
GTP binding	0.295705904888768	bayes_pls_golite062009
primary active transmembrane transporter activity	0.294474570607914	bayes_pls_golite062009
guanyl ribonucleotide binding	0.29028316917561	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	0.282352478532746	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.243902356228423	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	0.220608508617331	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	0.219533217661421	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	0.219157471322311	bayes_pls_golite062009
protein binding	0.170837278876362	bayes_pls_golite062009
microfilament motor activity	0.10236059675512	bayes_pls_golite062009
protein transporter activity	0.0397092337273124	bayes_pls_golite062009
cation transmembrane transporter activity	0.0254369227200564	bayes_pls_golite062009
signal sequence binding	6.53725193420218E-4	bayes_pls_golite062009

Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

Philius Transmembrane Prediction:

Protein predicted to be:	GLOBULAR (No transmembrane regions or signal peptide)
Confidence of classification:	0.99

Source: Reynolds et al. (2008)

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2