Reviewed, UniProtKB/Swiss-Prot P20095 (PRP2_YEAST)

Names and origin

Protein names

Recommended name:
    Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
    EC=3.6.1.-
Alternative name(s):
    Pre-mRNA-processing protein 2

Gene names

Name:	PRP2
Synonyms:	RNA2
Ordered Locus Names:	YNR011C
ORF Names:	N2048

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	876 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Involved in pre-mRNA splicing. Is required together with ATP and at least one other factor, for the first cleavage-ligation reaction. Functions as a molecular motor in the activation of the precatalytic spliceosome for the first transesterification reaction of pre-mRNA splicing by hydrolyzing ATP to cause the activation of the spliceosome without the occurrence of splicing. Capable of hydrolyzing nucleoside triphosphates in the presence of single-stranded RNAs such as poly(U). Ref.6 Ref.7 Ref.9 Ref.11 Ref.15
Subunit structure	Interacts directly with pre-mRNA. According to Ref.6, associated with spliceosomes prior to and throughout step 1 of the splicing reaction. According to Ref.11, it leaves the spliceosome before reaction 1. Interacts with SPP2. Ref.6 Ref.9 Ref.11 Ref.15 Ref.10 Ref.14
Subcellular location	Nucleus. Ref.5 Ref.12
Miscellaneous	Present with 172 molecules/cell in log phase SD medium. Ref.13
Sequence similarities	Belongs to the DEAD box helicase family. DEAH subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus
Ligand	ATP-binding Nucleotide-binding
Molecular function	Hydrolase
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	generation of catalytic spliceosome for first transesterification step Traceable author statement. Source: SGD
Cellular component	spliceosome 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 splicing factor activity, transesterification mechanism Traceable author statement. Source: SGD nucleic acid binding Inferred from electronic annotation. Source: InterPro protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
	P43582	1	EBI-13820,EBI-22766
ESS1	P22696	1	EBI-13820,EBI-6679
PRP40	P33203	1	EBI-13820,EBI-701
RSP5	P39940	1	EBI-13820,EBI-16219
URN1	Q06525	1	EBI-13820,EBI-35138

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 876	876	Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2		PRO_0000055130
Regions
	Domain	233 – 399	167	Helicase ATP-binding
	Domain	424 – 598	175	Helicase C-terminal
	Nucleotide binding	246 – 253	8	ATP By similarity
	Motif	346 – 349	4	DEAH box
Amino acid modifications
	Modified residue	284	1	Phosphothreonine Ref.16
Experimental info
	Mutagenesis	6 – 206	201	Missing: No affect on activity.
	Mutagenesis	89 – 552	464	Missing: Loss of ATPase and splicing activity.
	Mutagenesis	89 – 206	118	Missing: Wild-type RNA-dependent ATPase activity; bounds tightly to the spliceosome and after addition of ATP released from the spliceosome.
	Mutagenesis	349	1	H → D: Fails to release from the spliceosome; when associated with H-548. Ref.15
	Mutagenesis	378	1	S → L in PRP2-dn1; 40% of wild-type RNA-stimulated ATPase activity; splicing activity abolished; accumulates stalled splicing complexes. Ref.8
	Mutagenesis	548	1	Q → H: Fails to release from the spliceosome; when associated with D-349. Ref.15
	Mutagenesis	551	1	G → N: Fails to release from the spliceosome. Ref.15
	Mutagenesis	554 – 876	323	Missing: Has small amount of ATPase activity, but no splicing activity.
	Mutagenesis	615 – 876	262	Missing: Loss of activity.
	Mutagenesis	824 – 876	53	Missing: Spliceosome binding mutant; not active in splicing; when associated with N-551.
	Mutagenesis	833 – 876	44	Missing: Spliceosome binding mutant; not active in splicing; when associated with N-551.
	Mutagenesis	834 – 876	43	Missing: Spliceosome binding mutant; not active in splicing; when associated with N-551. Almost wild-type RNA-dependent ATPase activity.
	Mutagenesis	845 – 846	2	DC → NY: Spliceosome binding mutant; not active in splicing; when associated with N-551, or D-349 and H-548. Loss of interaction with SPP2. Ref.14
	Mutagenesis	845	1	D → L: Temperature-sensitive; decreased interaction with SPP2, decreased cell growth on benomyl and decreased splicing at elevated temperatures; when associated with D-349 and H-548. Ref.14
	Mutagenesis	854 – 855	2	WL → AA: Loss of interaction with SPP2.

Sequences

	Sequence		Length	Mass (Da)
	P20095-1 [UniParc]. Last modified February 1, 1991. Version 1. Checksum: 7EB3E1EE93215F57	FASTA	876	99,814
	10 20 30 40 50 60 MSSITSETGK RRVKRTYEVT RQNDNAVRIE PSSLGEEEDK EAKDKNSALQ LKRSRYDPNK 70 80 90 100 110 120 VFSNTNQGPE KNNLKGEQLG SQKKSSKYDE KITSNNELTT KKGLLGDSEN ETKYASSNSK 130 140 150 160 170 180 FNVEVTHKIK NAKEIDKINR QRMWEEQQLR NAMAGQSDHP DDITLEGSDK YDYVFDTDAM 190 200 210 220 230 240 IDYTNEEDDL LPEEKLQYEA RLAQALETEE KRILTIQEAR KLLPVHQYKD ELLQEIKKNQ 250 260 270 280 290 300 VLIIMGETGS GKTTQLPQYL VEDGFTDQGK LQIAITQPRR VAATSVAARV ADEMNVVLGK 310 320 330 340 350 360 EVGYQIRFED KTTPNKTVLK YMTDGMLLRE FLTDSKLSKY SCIMIDEAHE RTLATDILIG 370 380 390 400 410 420 LLKDILPQRP TLKLLISSAT MNAKKFSEFF DNCPIFNVPG RRYPVDIHYT LQPEANYIHA 430 440 450 460 470 480 AITTIFQIHT TQSLPGDILV FLTGQEEIER TKTKLEEIMS KLGSRTKQMI ITPIYANLPQ 490 500 510 520 530 540 EQQLKIFQPT PENCRKVVLA TNIAETSLTI DGIRYVIDPG FVKENSYVPS TGMTQLLTVP 550 560 570 580 590 600 CSRASVDQRA GRAGRVGPGK CFRIFTKWSY LHELELMPKP EITRTNLSNT VLLLLSLGVT 610 620 630 640 650 660 DLIKFPLMDK PSIPTLRKSL ENLYILGALN SKGTITRLGK MMCEFPCEPE FAKVLYTAAT 670 680 690 700 710 720 HEQCQGVLEE CLTIVSMLHE TPSLFIGQKR DAAASVLSEV ESDHILYLEI FNQWRNSKFS 730 740 750 760 770 780 RSWCQDHKIQ FKTMLRVRNI RNQLFRCSEK VGLVEKNDQA RMKIGNIAGY INARITRCFI 790 800 810 820 830 840 SGFPMNIVQL GPTGYQTMGR SSGGLNVSVH PTSILFVNHK EKAQRPSKYV LYQQLMLTSK 850 860 870 EFIRDCLVIP KEEWLIDMVP QIFKDLIDDK TNRGRR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The yeast PRP2 protein, a putative RNA-dependent ATPase, shares extensive sequence homology with two other pre-mRNA splicing factors." Chen J.H., Lin R.J. Nucleic Acids Res. 18:6447-6447(1990) [PubMed: 2147058] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Beggs J.D. Submitted (FEB-1990) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: DBY939.
[3]	"Twelve open reading frames revealed in the 23.6 kb segment flanking the centromere on the Saccharomyces cerevisiae chromosome XIV right arm." Verhasselt P., Aert R., Voet M., Volckaert G. Yeast 10:1355-1361(1994) [PubMed: 7900425] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J. Nature 387:93-98(1997) [PubMed: 9169873] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[5]	"Identification and nuclear localization of yeast pre-messenger RNA processing components: RNA2 and RNA3 proteins." Last R.L., Woolford J.L. Jr. J. Cell Biol. 103:2103-2112(1986) [PubMed: 3536958] [Abstract] Cited for: SUBCELLULAR LOCATION.
[6]	"Interactions of PRP2 protein with pre-mRNA splicing complexes in Saccharomyces cerevisiae." King D.S., Beggs J.D. Nucleic Acids Res. 18:6559-6564(1990) [PubMed: 2251118] [Abstract] Cited for: FUNCTION, INTERACTION WITH SPLICEOSOME.
[7]	"The purified yeast pre-mRNA splicing factor PRP2 is an RNA-dependent NTPase." Kim S.-H., Smith J., Claude A., Lin R.-J. EMBO J. 11:2319-2326(1992) [PubMed: 1534753] [Abstract] Cited for: FUNCTION AS A NTPASE, LACK OF HELICASE ACTIVITY.
[8]	"A dominant negative mutation in the conserved RNA helicase motif 'SAT' causes splicing factor PRP2 to stall in spliceosomes." Plumpton M., McGarvey M., Beggs J.D. EMBO J. 13:879-887(1994) [PubMed: 8112301] [Abstract] Cited for: MUTAGENESIS OF SER-378.
[9]	"The splicing factor PRP2, a putative RNA helicase, interacts directly with pre-mRNA." Teigelkamp S., McGarvey M., Plumpton M., Beggs J.D. EMBO J. 13:888-897(1994) [PubMed: 8112302] [Abstract] Cited for: FUNCTION, INTERACTION WITH PRE-MRNA.
[10]	"The final stages of spliceosome maturation require Spp2p that can interact with the DEAH box protein Prp2p and promote step 1 of splicing." Roy J., Kim K., Maddock J.R., Anthony J.G., Woolford J.L. Jr. RNA 1:375-390(1995) [PubMed: 7493316] [Abstract] Cited for: INTERACTION WITH SPP2.
[11]	"Spliceosome activation by PRP2 ATPase prior to the first transesterification reaction of pre-mRNA splicing." Kim S.-H., Lin R.-J. Mol. Cell. Biol. 16:6810-6819(1996) [PubMed: 8943336] [Abstract] Cited for: FUNCTION AS AN ATPASE, INTERACTION WITH SPLICEOSOME.
[12]	"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].
[13]	"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].
[14]	"Interaction between a G-patch protein and a spliceosomal DEXD/H-box ATPase that is critical for splicing." Silverman E.J., Maeda A., Wei J., Smith P., Beggs J.D., Lin R.-J. Mol. Cell. Biol. 24:10101-10110(2004) [PubMed: 15542821] [Abstract] Cited for: INTERACTION WITH SPP2, MUTAGENESIS OF ASP-845; 845-ASP-CYS-846 AND 854-TRP-LEU-855.
[15]	"Definition of a spliceosome interaction domain in yeast Prp2 ATPase." Edwalds-Gilbert G., Kim D.-H., Silverman E., Lin R.-J. RNA 10:210-220(2004) [PubMed: 14730020] [Abstract] Cited for: FUNCTION AS AN ATPASE, INTERACTION WITH SPLICEOSOME, DELETION MUTANTS, MUTAGENESIS OF HIS-349; GLN-548; GLY-551 AND 845-ASP-CYS-846.
[16]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-284, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X55936 Genomic DNA. Translation: CAA39401.1. X55999 Genomic DNA. Translation: CAA39471.1. X77395 Genomic DNA. Translation: CAA54579.1. Z71626 Genomic DNA. Translation: CAA96288.1.
PIR	S12334.
RefSeq	NP_014408.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:3961N.
IntAct	P20095. 8 interactions.
Genome annotation databases
Ensembl	YNR011C. Saccharomyces cerevisiae. [Contig view]
GeneID	855745.
GenomeReviews	Gene locus YNR011C in contig Y13139_GR.
KEGG	sce:YNR011C.
NMPDR	fig|4932.3.peg.5488.
Organism-specific databases
CYGD	YNR011c.
SGD	S000005294. PRP2.
Yeast-GFP	Search...
Phylogenomic databases
HOGENOM	P20095.
OMA	P20095. TSKVDTN.
Gene expression databases
ArrayExpress	P20095.
GermOnline	YNR011C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR014001. DEAD-like_N. IPR001650. DNA/RNA_helicase_C. IPR002464. DNA/RNA_helicase_DEAH_CS. IPR011709. DUF1605. IPR007502. Helicase-assoc_reg. IPR014021. Helicase_SF1/SF2_ATP-bd. [Graphical view]
Pfam	PF07717. DUF1605. 1 hit. PF04408. HA2. 1 hit. PF00271. Helicase_C. 1 hit. [Graphical view]
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
PROSITE	PS00690. DEAH_ATP_HELICASE. 1 hit. PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	980148.

Entry information

Entry name

PRP2_YEAST

Accession

Primary (citable) accession number: P20095

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1991
Last sequence update:	February 1, 1991
Last modified:	June 16, 2009
This is version 96 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)