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Protein

Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2

Gene

PRP2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).5 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi246 – 2538ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

  • generation of catalytic spliceosome for first transesterification step Source: SGD
  • snoRNA splicing Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33328-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 (EC:3.6.4.13)
Alternative name(s):
Pre-mRNA-processing protein 2
Gene namesi
Name:PRP2
Synonyms:RNA2
Ordered Locus Names:YNR011C
ORF Names:N2048
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNR011C.
SGDiS000005294. PRP2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi6 – 206201Missing : No affect on activity. Add
BLAST
Mutagenesisi89 – 552464Missing : Loss of ATPase and splicing activity. Add
BLAST
Mutagenesisi89 – 206118Missing : Wild-type RNA-dependent ATPase activity; bound tightly to the spliceosome and after addition of ATP released from the spliceosome. Add
BLAST
Mutagenesisi349 – 3491H → D: Fails to release from the spliceosome; when associated with H-548. 1 Publication
Mutagenesisi378 – 3781S → L in PRP2-dn1; 40% of wild-type RNA-stimulated ATPase activity; splicing activity abolished; accumulates stalled splicing complexes. 1 Publication
Mutagenesisi548 – 5481Q → H: Fails to release from the spliceosome; when associated with D-349. 1 Publication
Mutagenesisi551 – 5511G → N: Fails to release from the spliceosome. 1 Publication
Mutagenesisi554 – 876323Missing : Has small amount of ATPase activity, but no splicing activity. Add
BLAST
Mutagenesisi615 – 876262Missing : Loss of activity. Add
BLAST
Mutagenesisi824 – 87653Missing : Spliceosome binding mutant; not active in splicing; when associated with N-551. Add
BLAST
Mutagenesisi833 – 87644Missing : Spliceosome binding mutant; not active in splicing; when associated with N-551. Add
BLAST
Mutagenesisi834 – 87643Missing : Spliceosome binding mutant; not active in splicing; when associated with N-551. Almost wild-type RNA-dependent ATPase activity. Add
BLAST
Mutagenesisi845 – 8462DC → NY: Spliceosome binding mutant; not active in splicing; when associated with N-551, or D-349 and H-548. Loss of interaction with SPP2. 2 Publications
Mutagenesisi845 – 8451D → 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. 1 Publication
Mutagenesisi854 – 8552WL → AA: Loss of interaction with SPP2. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 876875Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2PRO_0000055130Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP20095.

PTM databases

iPTMnetiP20095.

Interactioni

Subunit structurei

Interacts directly with pre-mRNA. According to PubMed:2251118, associated with spliceosomes prior to and throughout step 1 of the splicing reaction. According to PubMed:8943336, it leaves the spliceosome before reaction 1. Interacts with SPP2.6 Publications

Protein-protein interaction databases

BioGridi35836. 85 interactions.
DIPiDIP-3961N.
IntActiP20095. 8 interactions.
MINTiMINT-496813.

Structurei

3D structure databases

ProteinModelPortaliP20095.
SMRiP20095. Positions 212-863.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini233 – 399167Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini424 – 598175Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi346 – 3494DEAH box

Sequence similaritiesi

Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00840000131463.
HOGENOMiHOG000175261.
InParanoidiP20095.
KOiK12814.
OMAiCEPEFAK.
OrthoDBiEOG7M98QW.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR002464. DNA/RNA_helicase_DEAH_CS.
IPR011709. DUF1605.
IPR007502. Helicase-assoc_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF04408. HA2. 1 hit.
PF00271. Helicase_C. 1 hit.
PF07717. OB_NTP_bind. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00847. HA2. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00690. DEAH_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P20095-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSITSETGK RRVKRTYEVT RQNDNAVRIE PSSLGEEEDK EAKDKNSALQ
60 70 80 90 100
LKRSRYDPNK VFSNTNQGPE KNNLKGEQLG SQKKSSKYDE KITSNNELTT
110 120 130 140 150
KKGLLGDSEN ETKYASSNSK FNVEVTHKIK NAKEIDKINR QRMWEEQQLR
160 170 180 190 200
NAMAGQSDHP DDITLEGSDK YDYVFDTDAM IDYTNEEDDL LPEEKLQYEA
210 220 230 240 250
RLAQALETEE KRILTIQEAR KLLPVHQYKD ELLQEIKKNQ VLIIMGETGS
260 270 280 290 300
GKTTQLPQYL VEDGFTDQGK LQIAITQPRR VAATSVAARV ADEMNVVLGK
310 320 330 340 350
EVGYQIRFED KTTPNKTVLK YMTDGMLLRE FLTDSKLSKY SCIMIDEAHE
360 370 380 390 400
RTLATDILIG LLKDILPQRP TLKLLISSAT MNAKKFSEFF DNCPIFNVPG
410 420 430 440 450
RRYPVDIHYT LQPEANYIHA AITTIFQIHT TQSLPGDILV FLTGQEEIER
460 470 480 490 500
TKTKLEEIMS KLGSRTKQMI ITPIYANLPQ EQQLKIFQPT PENCRKVVLA
510 520 530 540 550
TNIAETSLTI DGIRYVIDPG FVKENSYVPS TGMTQLLTVP CSRASVDQRA
560 570 580 590 600
GRAGRVGPGK CFRIFTKWSY LHELELMPKP EITRTNLSNT VLLLLSLGVT
610 620 630 640 650
DLIKFPLMDK PSIPTLRKSL ENLYILGALN SKGTITRLGK MMCEFPCEPE
660 670 680 690 700
FAKVLYTAAT HEQCQGVLEE CLTIVSMLHE TPSLFIGQKR DAAASVLSEV
710 720 730 740 750
ESDHILYLEI FNQWRNSKFS RSWCQDHKIQ FKTMLRVRNI RNQLFRCSEK
760 770 780 790 800
VGLVEKNDQA RMKIGNIAGY INARITRCFI SGFPMNIVQL GPTGYQTMGR
810 820 830 840 850
SSGGLNVSVH PTSILFVNHK EKAQRPSKYV LYQQLMLTSK EFIRDCLVIP
860 870
KEEWLIDMVP QIFKDLIDDK TNRGRR
Length:876
Mass (Da):99,814
Last modified:February 1, 1991 - v1
Checksum:i7EB3E1EE93215F57
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X55936 Genomic DNA. Translation: CAA39401.1.
X55999 Genomic DNA. Translation: CAA39471.1.
X77395 Genomic DNA. Translation: CAA54579.1.
Z71626 Genomic DNA. Translation: CAA96288.1.
BK006947 Genomic DNA. Translation: DAA10552.1.
PIRiS12334.
RefSeqiNP_014408.1. NM_001183188.1.

Genome annotation databases

EnsemblFungiiYNR011C; YNR011C; YNR011C.
GeneIDi855745.
KEGGisce:YNR011C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X55936 Genomic DNA. Translation: CAA39401.1.
X55999 Genomic DNA. Translation: CAA39471.1.
X77395 Genomic DNA. Translation: CAA54579.1.
Z71626 Genomic DNA. Translation: CAA96288.1.
BK006947 Genomic DNA. Translation: DAA10552.1.
PIRiS12334.
RefSeqiNP_014408.1. NM_001183188.1.

3D structure databases

ProteinModelPortaliP20095.
SMRiP20095. Positions 212-863.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35836. 85 interactions.
DIPiDIP-3961N.
IntActiP20095. 8 interactions.
MINTiMINT-496813.

PTM databases

iPTMnetiP20095.

Proteomic databases

MaxQBiP20095.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNR011C; YNR011C; YNR011C.
GeneIDi855745.
KEGGisce:YNR011C.

Organism-specific databases

EuPathDBiFungiDB:YNR011C.
SGDiS000005294. PRP2.

Phylogenomic databases

GeneTreeiENSGT00840000131463.
HOGENOMiHOG000175261.
InParanoidiP20095.
KOiK12814.
OMAiCEPEFAK.
OrthoDBiEOG7M98QW.

Enzyme and pathway databases

BioCyciYEAST:G3O-33328-MONOMER.

Miscellaneous databases

PROiP20095.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR002464. DNA/RNA_helicase_DEAH_CS.
IPR011709. DUF1605.
IPR007502. Helicase-assoc_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF04408. HA2. 1 hit.
PF00271. Helicase_C. 1 hit.
PF07717. OB_NTP_bind. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00847. HA2. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00690. DEAH_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. "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] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  7. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH SPLICEOSOME.
  8. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A NTPASE, LACK OF HELICASE ACTIVITY.
  9. "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] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF SER-378.
  10. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH PRE-MRNA.
  11. "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] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SPP2.
  12. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS AN ATPASE, INTERACTION WITH SPLICEOSOME.
  13. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  14. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  15. "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] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SPP2, MUTAGENESIS OF ASP-845; 845-ASP-CYS-846 AND 854-TRP-LEU-855.
  16. "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] [Europe PMC] [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.
  17. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiPRP2_YEAST
AccessioniPrimary (citable) accession number: P20095
Secondary accession number(s): D6W1I6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: February 1, 1991
Last modified: July 6, 2016
This is version 165 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 172 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.