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Protein

Pre-mRNA-splicing ATP-dependent RNA helicase PRP28

Gene

PRP28

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

ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.3 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi221 – 2288ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: SGD
  • first spliceosomal transesterification activity Source: SGD
  • RNA binding Source: SGD

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29816-MONOMER.
ReactomeiR-SCE-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC:3.6.4.13)
Alternative name(s):
Helicase CA8
Gene namesi
Name:PRP28
Ordered Locus Names:YDR243C
ORF Names:YD8419.10C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR243C.
SGDiS000002651. PRP28.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic ribonucleoprotein granule Source: GO_Central
  • U5 snRNP Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi221 – 2211A → V in PRP28-103; no growth at 15 and 37 degrees Celsius. 1 Publication
Mutagenesisi223 – 2231T → I in PRP28-117; no growth at 15 degrees Celsius. 1 Publication
Mutagenesisi264 – 2641R → D or E: Lethal. 1 Publication
Mutagenesisi265 – 2651E → Q in PRP28-99; no growth at 15 and 37 degrees Celsius. 1 Publication
Mutagenesisi297 – 2971G → E in PRP28-1; no growth at 15 degrees Celsius. 1 Publication
Mutagenesisi317 – 3171T → I in PRP28-36; slow growth at 30 degrees Celsius, and no growth at 15 and 37 degrees Celsius. 1 Publication
Mutagenesisi317 – 3171T → Y: Lethal. 1 Publication
Mutagenesisi319 – 3191G → E or V: No growth at 15 and 37 degrees Celsius. 1 Publication
Mutagenesisi376 – 3761M → I in PRP28-32; no growth at 15 degrees Celsius. 1 Publication
Mutagenesisi379 – 3791A → W in PRP28-102; no growth at 25 degrees Celsius or lower. 1 Publication
Mutagenesisi438 – 4381P → L in PRP28-61; no growth at 37 degrees Celsius; when associated with L-468 and D-486. 1 Publication
Mutagenesisi440 – 4401I → F in PRP28-56; no growth at 37 degrees Celsius; when associated with S-546 and E-584. 1 Publication
Mutagenesisi442 – 4421F → G in PRP28-101; no growth at 15 and 37 degrees Celsius. 1 Publication
Mutagenesisi442 – 4421F → S in PRP28-55; no growth at 37 degrees Celsius. 1 Publication
Mutagenesisi449 – 4491A → T in PRP28-66; no growth at 37 degrees Celsius; when associated with A-541; V-549; N-580 and V-586. 1 Publication
Mutagenesisi468 – 4681H → L in PRP28-61; no growth at 37 degrees Celsius; when associated with L-438 and D-486. 1 Publication
Mutagenesisi486 – 4861N → D in PRP28-61; no growth at 37 degrees Celsius; when associated with L-438 and L-468. 1 Publication
Mutagenesisi491 – 4911M → K in PRP28-52; no growth at 37 degrees Celsius. 1 Publication
Mutagenesisi499 – 4991R → G in PRP28-86; lethal. 1 Publication
Mutagenesisi499 – 4991R → K: No growth at 15 degrees Celsius. 1 Publication
Mutagenesisi502 – 5021D → N: Lethal. 1 Publication
Mutagenesisi521 – 5211Y → D in PRP28-37; no growth at 37 degrees Celsius. 1 Publication
Mutagenesisi527 – 5271R → D: Lethal. 1 Publication
Mutagenesisi541 – 5411V → A in PRP28-66; no growth at 37 degrees Celsius; when associated with T-449; V-549; N-580 and V-586. 1 Publication
Mutagenesisi546 – 5461D → S in PRP28-56; no growth at 37 degrees Celsius; when associated with F-440 and E-584. 1 Publication
Mutagenesisi549 – 5491L → V in PRP28-66; no growth at 37 degrees Celsius; when associated with T-449; A-541; N-580 and V-586. 1 Publication
Mutagenesisi580 – 5801K → N in PRP28-66; no growth at 37 degrees Celsius; when associated with T-449; A-541; V-549 and V-586. 1 Publication
Mutagenesisi584 – 5841N → E in PRP28-56; no growth at 37 degrees Celsius; when associated with F-440 and S-546. 1 Publication
Mutagenesisi586 – 5861I → V in PRP28-66; no growth at 37 degrees Celsius; when associated with T-449; A-541; V-549 and N-580. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 588588Pre-mRNA-splicing ATP-dependent RNA helicase PRP28PRO_0000055127Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei69 – 691PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP23394.

PTM databases

iPTMnetiP23394.

Interactioni

Subunit structurei

Component of the U5 snRNP complex, composed of at least BRR2, PRP8, PRP28, DIB1, LIN1, SMB1, SMD1, SMD2, SMD3, SME1, SMX2, SMX3, and SNU114, associated with the U5 snRNA.1 Publication

Protein-protein interaction databases

BioGridi32294. 82 interactions.
DIPiDIP-6324N.
IntActiP23394. 17 interactions.
MINTiMINT-599541.

Structurei

Secondary structure

1
588
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi138 – 1403Combined sources
Helixi143 – 1453Combined sources
Helixi148 – 15710Combined sources
Beta strandi160 – 1667Combined sources
Beta strandi172 – 1754Combined sources
Helixi182 – 1909Combined sources
Helixi199 – 20810Combined sources
Beta strandi217 – 2204Combined sources
Helixi227 – 24014Combined sources
Helixi247 – 2537Combined sources
Beta strandi256 – 2605Combined sources
Helixi264 – 28320Combined sources
Beta strandi284 – 2863Combined sources
Beta strandi291 – 2944Combined sources
Helixi300 – 3078Combined sources
Beta strandi312 – 3165Combined sources
Helixi318 – 3269Combined sources
Beta strandi337 – 3404Combined sources
Helixi343 – 3486Combined sources
Helixi352 – 36514Combined sources
Beta strandi373 – 3808Combined sources
Helixi383 – 39210Combined sources
Beta strandi397 – 4037Combined sources
Beta strandi410 – 4178Combined sources
Helixi421 – 43212Combined sources
Beta strandi439 – 4424Combined sources
Helixi446 – 45914Combined sources
Beta strandi464 – 4674Combined sources
Helixi473 – 48412Combined sources
Beta strandi487 – 4937Combined sources
Turni495 – 5006Combined sources
Beta strandi506 – 5138Combined sources
Helixi518 – 5258Combined sources
Beta strandi534 – 5418Combined sources
Helixi547 – 55913Combined sources
Helixi570 – 5767Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4W7SX-ray2.54A/B127-588[»]
ProteinModelPortaliP23394.
SMRiP23394. Positions 134-588.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini208 – 399192Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini427 – 579153Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi172 – 20231Q motifAdd
BLAST
Motifi341 – 3444DEAD box

Domaini

The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00820000127023.
HOGENOMiHOG000268796.
InParanoidiP23394.
KOiK12858.
OMAiATISPPI.
OrthoDBiEOG092C1KT9.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P23394-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARPIDVSQL IAGINKKKGL DENTSGKISK PRFLNKQERS KQERLKENEE
60 70 80 90 100
SLTPTQSDSA KVEIKKVNSR DDSFFNETND KKRNPSKQNG SKFHFSWNES
110 120 130 140 150
EDTLSGYDPI VSTRAIDLLW KGKTPKNAAE SSYMGKHWTE KSLHEMNERD
160 170 180 190 200
WRILKEDYAI VTKGGTVENP LRNWEELNII PRDLLRVIIQ ELRFPSPTPI
210 220 230 240 250
QRITIPNVCN MKQYRDFLGV ASTGSGKTLA FVIPILIKMS RSPPRPPSLK
260 270 280 290 300
IIDGPKALIL APTRELVQQI QKETQKVTKI WSKESNYDCK VISIVGGHSL
310 320 330 340 350
EEISFSLSEG CDILVATPGR LIDSLENHLL VMKQVETLVL DEADKMIDLG
360 370 380 390 400
FEDQVTNILT KVDINADSAV NRQTLMFTAT MTPVIEKIAA GYMQKPVYAT
410 420 430 440 450
IGVETGSEPL IQQVVEYADN DEDKFKKLKP IVAKYDPPII IFINYKQTAD
460 470 480 490 500
WLAEKFQKET NMKVTILHGS KSQEQREHSL QLFRTNKVQI MIATNVAARG
510 520 530 540 550
LDIPNVSLVV NFQISKKMDD YIHRIGRTGR AANEGTAVSF VSAAEDESLI
560 570 580
RELYKYVRKH DPLNSNIFSE AVKNKYNVGK QLSNEIIY
Length:588
Mass (Da):66,641
Last modified:November 1, 1995 - v2
Checksum:i333ADBF9D7C75C99
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti493 – 4931A → R no nucleotide entry (PubMed:2406722).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56934 Genomic DNA. Translation: CAA40255.1.
Z49701 Genomic DNA. Translation: CAA89729.1.
BK006938 Genomic DNA. Translation: DAA12083.1.
PIRiA39624.
RefSeqiNP_010529.3. NM_001180551.3.

Genome annotation databases

EnsemblFungiiYDR243C; YDR243C; YDR243C.
GeneIDi851830.
KEGGisce:YDR243C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56934 Genomic DNA. Translation: CAA40255.1.
Z49701 Genomic DNA. Translation: CAA89729.1.
BK006938 Genomic DNA. Translation: DAA12083.1.
PIRiA39624.
RefSeqiNP_010529.3. NM_001180551.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4W7SX-ray2.54A/B127-588[»]
ProteinModelPortaliP23394.
SMRiP23394. Positions 134-588.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32294. 82 interactions.
DIPiDIP-6324N.
IntActiP23394. 17 interactions.
MINTiMINT-599541.

PTM databases

iPTMnetiP23394.

Proteomic databases

MaxQBiP23394.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR243C; YDR243C; YDR243C.
GeneIDi851830.
KEGGisce:YDR243C.

Organism-specific databases

EuPathDBiFungiDB:YDR243C.
SGDiS000002651. PRP28.

Phylogenomic databases

GeneTreeiENSGT00820000127023.
HOGENOMiHOG000268796.
InParanoidiP23394.
KOiK12858.
OMAiATISPPI.
OrthoDBiEOG092C1KT9.

Enzyme and pathway databases

BioCyciYEAST:G3O-29816-MONOMER.
ReactomeiR-SCE-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

PROiP23394.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPRP28_YEAST
AccessioniPrimary (citable) accession number: P23394
Secondary accession number(s): D6VSM3, P20450
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: November 1, 1995
Last modified: September 7, 2016
This is version 164 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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