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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)DescriptionActionsGraphical viewLength
Nucleotide bindingi221 – 228ATPPROSITE-ProRule annotation8

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)DescriptionActionsGraphical viewLength
Mutagenesisi221A → V in PRP28-103; no growth at 15 and 37 degrees Celsius. 1 Publication1
Mutagenesisi223T → I in PRP28-117; no growth at 15 degrees Celsius. 1 Publication1
Mutagenesisi264R → D or E: Lethal. 1 Publication1
Mutagenesisi265E → Q in PRP28-99; no growth at 15 and 37 degrees Celsius. 1 Publication1
Mutagenesisi297G → E in PRP28-1; no growth at 15 degrees Celsius. 1 Publication1
Mutagenesisi317T → I in PRP28-36; slow growth at 30 degrees Celsius, and no growth at 15 and 37 degrees Celsius. 1 Publication1
Mutagenesisi317T → Y: Lethal. 1 Publication1
Mutagenesisi319G → E or V: No growth at 15 and 37 degrees Celsius. 1 Publication1
Mutagenesisi376M → I in PRP28-32; no growth at 15 degrees Celsius. 1 Publication1
Mutagenesisi379A → W in PRP28-102; no growth at 25 degrees Celsius or lower. 1 Publication1
Mutagenesisi438P → L in PRP28-61; no growth at 37 degrees Celsius; when associated with L-468 and D-486. 1 Publication1
Mutagenesisi440I → F in PRP28-56; no growth at 37 degrees Celsius; when associated with S-546 and E-584. 1 Publication1
Mutagenesisi442F → G in PRP28-101; no growth at 15 and 37 degrees Celsius. 1 Publication1
Mutagenesisi442F → S in PRP28-55; no growth at 37 degrees Celsius. 1 Publication1
Mutagenesisi449A → T in PRP28-66; no growth at 37 degrees Celsius; when associated with A-541; V-549; N-580 and V-586. 1 Publication1
Mutagenesisi468H → L in PRP28-61; no growth at 37 degrees Celsius; when associated with L-438 and D-486. 1 Publication1
Mutagenesisi486N → D in PRP28-61; no growth at 37 degrees Celsius; when associated with L-438 and L-468. 1 Publication1
Mutagenesisi491M → K in PRP28-52; no growth at 37 degrees Celsius. 1 Publication1
Mutagenesisi499R → G in PRP28-86; lethal. 1 Publication1
Mutagenesisi499R → K: No growth at 15 degrees Celsius. 1 Publication1
Mutagenesisi502D → N: Lethal. 1 Publication1
Mutagenesisi521Y → D in PRP28-37; no growth at 37 degrees Celsius. 1 Publication1
Mutagenesisi527R → D: Lethal. 1 Publication1
Mutagenesisi541V → A in PRP28-66; no growth at 37 degrees Celsius; when associated with T-449; V-549; N-580 and V-586. 1 Publication1
Mutagenesisi546D → S in PRP28-56; no growth at 37 degrees Celsius; when associated with F-440 and E-584. 1 Publication1
Mutagenesisi549L → V in PRP28-66; no growth at 37 degrees Celsius; when associated with T-449; A-541; N-580 and V-586. 1 Publication1
Mutagenesisi580K → N in PRP28-66; no growth at 37 degrees Celsius; when associated with T-449; A-541; V-549 and V-586. 1 Publication1
Mutagenesisi584N → E in PRP28-56; no growth at 37 degrees Celsius; when associated with F-440 and S-546. 1 Publication1
Mutagenesisi586I → V in PRP28-66; no growth at 37 degrees Celsius; when associated with T-449; A-541; V-549 and N-580. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000551271 – 588Pre-mRNA-splicing ATP-dependent RNA helicase PRP28Add BLAST588

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei69PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP23394.
PRIDEiP23394.

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 interactors.
DIPiDIP-6324N.
IntActiP23394. 17 interactors.
MINTiMINT-599541.

Structurei

Secondary structure

1588
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi138 – 140Combined sources3
Helixi143 – 145Combined sources3
Helixi148 – 157Combined sources10
Beta strandi160 – 166Combined sources7
Beta strandi172 – 175Combined sources4
Helixi182 – 190Combined sources9
Helixi199 – 208Combined sources10
Beta strandi217 – 220Combined sources4
Helixi227 – 240Combined sources14
Helixi247 – 253Combined sources7
Beta strandi256 – 260Combined sources5
Helixi264 – 283Combined sources20
Beta strandi284 – 286Combined sources3
Beta strandi291 – 294Combined sources4
Helixi300 – 307Combined sources8
Beta strandi312 – 316Combined sources5
Helixi318 – 326Combined sources9
Beta strandi337 – 340Combined sources4
Helixi343 – 348Combined sources6
Helixi352 – 365Combined sources14
Beta strandi373 – 380Combined sources8
Helixi383 – 392Combined sources10
Beta strandi397 – 403Combined sources7
Beta strandi410 – 417Combined sources8
Helixi421 – 432Combined sources12
Beta strandi439 – 442Combined sources4
Helixi446 – 459Combined sources14
Beta strandi464 – 467Combined sources4
Helixi473 – 484Combined sources12
Beta strandi487 – 493Combined sources7
Turni495 – 500Combined sources6
Beta strandi506 – 513Combined sources8
Helixi518 – 525Combined sources8
Beta strandi534 – 541Combined sources8
Helixi547 – 559Combined sources13
Helixi570 – 576Combined sources7

3D structure databases

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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini208 – 399Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST192
Domaini427 – 579Helicase C-terminalPROSITE-ProRule annotationAdd BLAST153

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi172 – 202Q motifAdd BLAST31
Motifi341 – 344DEAD box4

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)DescriptionActionsGraphical viewLength
Sequence conflicti493A → R no nucleotide entry (PubMed:2406722).Curated1

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4W7SX-ray2.54A/B127-588[»]
ProteinModelPortaliP23394.
SMRiP23394.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiP23394.

Proteomic databases

MaxQBiP23394.
PRIDEiP23394.

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: November 2, 2016
This is version 166 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.