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Protein

Pre-mRNA-processing protein PRP40

Gene

PRP40

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

Required for pre-spliceosome formation, which is the first step of pre-mRNA splicing. This protein is associated with snRNP U1. Two commitment complexes, CC1 and CC2, have been defined in yeast. CC1 is a basal complex dependent only on the 5' splice site. CC2 is a complex of lower mobility and is dependent on a branchpoint as well as a 5' splice site region. This protein is involved in CC2 formation where it binds to the branchpoint binding protein MSL5, bridging the U1 snRNP-associated 5' splice site and the MSL5-associated branch point 3' intron splice site.3 Publications

GO - Molecular functioni

  • RNA binding Source: SGD

GO - Biological processi

  • mRNA splicing, via spliceosome Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

BioCyciYEAST:G3O-31821-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-processing protein PRP40
Gene namesi
Name:PRP40
Ordered Locus Names:YKL012W
ORF Names:YKL165
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKL012W.
SGDiS000001495. PRP40.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

  • nucleus Source: SGD
  • U1 snRNP Source: SGD
  • U2-type prespliceosome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi240S → P in PRP40-1 suppressor; affects SAR1 mRNA accumulation in U1-U4 mutant at 18 degrees Celsius. 1 Publication1
Mutagenesisi274L → A: Temperature sensitive growth at 36 degrees Celsius. 1 Publication1
Mutagenesisi277L → A: Temperature sensitive growth at 36 degrees Celsius. 1 Publication1
Mutagenesisi281L → A: Temperature sensitive growth at 36 degrees Celsius. 1 Publication1
Mutagenesisi340L → A: Wild-type growth at 36 degrees Celsius. 1 Publication1
Mutagenesisi344L → A: Wild-type growth at 36 degrees Celsius. 1 Publication1
Mutagenesisi347L → I: Wild-type growth at 36 degrees Celsius. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000760841 – 583Pre-mRNA-processing protein PRP40Add BLAST583

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei576PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP33203.
PRIDEiP33203.

PTM databases

iPTMnetiP33203.

Interactioni

Subunit structurei

Interacts with CRM1, MSL5, PRP8, and the RNA polymerase II largest subunit (RPB1). MSL5, MUD2 and PRP40 interact to form the commitment complex 2 (CC2), a precursor of mature spliceosomes.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ADE12P802102EBI-701,EBI-14267
AMD1P152742EBI-701,EBI-2548
FMP40Q089682EBI-701,EBI-29375
GPH1P067382EBI-701,EBI-13389
LHP1P333992EBI-701,EBI-10046
MLS1P309522EBI-701,EBI-10428
NPT1P396832EBI-701,EBI-12218
PCK1P109632EBI-701,EBI-13770
SNU71P532075EBI-701,EBI-736
STM1P390152EBI-701,EBI-11238
YDL086WQ075052EBI-701,EBI-5951
YJR096WP471372EBI-701,EBI-25572

Protein-protein interaction databases

BioGridi34120. 144 interactors.
DIPiDIP-1620N.
IntActiP33203. 118 interactors.
MINTiMINT-386201.

Structurei

Secondary structure

1583
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 8Combined sources5
Beta strandi14 – 18Combined sources5
Turni19 – 22Combined sources4
Beta strandi23 – 27Combined sources5
Helixi30 – 43Combined sources14
Beta strandi46 – 49Combined sources4
Beta strandi55 – 59Combined sources5
Turni60 – 63Combined sources4
Beta strandi64 – 68Combined sources5
Helixi134 – 145Combined sources12
Helixi154 – 164Combined sources11
Helixi167 – 170Combined sources4
Helixi175 – 187Combined sources13
Helixi489 – 507Combined sources19
Beta strandi510 – 513Combined sources4
Helixi519 – 526Combined sources8
Helixi533 – 535Combined sources3
Helixi539 – 549Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1O6WNMR-A1-75[»]
2B7ENMR-A134-189[»]
2KFDNMR-A488-552[»]
ProteinModelPortaliP33203.
SMRiP33203.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP33203.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 31WW 1PROSITE-ProRule annotationAdd BLAST31
Domaini42 – 72WW 2PROSITE-ProRule annotationAdd BLAST31
Domaini132 – 188FF 1Add BLAST57
Domaini201 – 257FF 2Add BLAST57
Domaini262 – 332FF 3Add BLAST71
Domaini354 – 413FF 4Add BLAST60
Domaini427 – 488FF 5Add BLAST62
Domaini491 – 552FF 6Add BLAST62

Domaini

The WW and FF domains bind to the phosphorylated carboxy-terminal domain of RPB1.

Sequence similaritiesi

Belongs to the PRPF40 family.Curated
Contains 6 FF domains.Curated
Contains 2 WW domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00820000127014.
HOGENOMiHOG000001088.
InParanoidiP33203.
KOiK12821.
OMAiRDPRYWM.
OrthoDBiEOG092C1L62.

Family and domain databases

Gene3Di1.10.10.440. 3 hits.
InterProiIPR002713. FF_domain.
IPR001202. WW_dom.
[Graphical view]
PfamiPF01846. FF. 3 hits.
PF00397. WW. 2 hits.
[Graphical view]
SMARTiSM00441. FF. 4 hits.
SM00456. WW. 2 hits.
[Graphical view]
SUPFAMiSSF51045. SSF51045. 2 hits.
SSF81698. SSF81698. 3 hits.
PROSITEiPS51676. FF. 6 hits.
PS01159. WW_DOMAIN_1. 2 hits.
PS50020. WW_DOMAIN_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P33203-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSIWKEAKDA SGRIYYYNTL TKKSTWEKPK ELISQEELLL RENGWKAAKT
60 70 80 90 100
ADGKVYYYNP TTRETSWTIP AFEKKVEPIA EQKHDTVSHA QVNGNRIALT
110 120 130 140 150
AGEKQEPGRT INEEESQYAN NSKLLNVRRR TKEEAEKEFI TMLKENQVDS
160 170 180 190 200
TWSFSRIISE LGTRDPRYWM VDDDPLWKKE MFEKYLSNRS ADQLLKEHNE
210 220 230 240 250
TSKFKEAFQK MLQNNSHIKY YTRWPTAKRL IADEPIYKHS VVNEKTKRQT
260 270 280 290 300
FQDYIDTLID TQKESKKKLK TQALKELREY LNGIITTSSS ETFITWQQLL
310 320 330 340 350
NHYVFDKSKR YMANRHFKVL THEDVLNEYL KIVNTIENDL QNKLNELRLR
360 370 380 390 400
NYTRDRIARD NFKSLLREVP IKIKANTRWS DIYPHIKSDP RFLHMLGRNG
410 420 430 440 450
SSCLDLFLDF VDEQRMYIFA QRSIAQQTLI DQNFEWNDAD SDEITKQNIE
460 470 480 490 500
KVLENDRKFD KVDKEDISLI VDGLIKQRNE KIQQKLQNER RILEQKKHYF
510 520 530 540 550
WLLLQRTYTK TGKPKPSTWD LASKELGESL EYKALGDEDN IRRQIFEDFK
560 570 580
PESSAPTAES ATANLTLTAS KKRHLTPAVE LDY
Length:583
Mass (Da):69,065
Last modified:February 1, 1994 - v1
Checksum:iBA1C1C91D532524C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S53418 Genomic DNA. Translation: AAB24902.1.
Z28012 Genomic DNA. Translation: CAA81847.1.
BK006944 Genomic DNA. Translation: DAA09144.1.
PIRiS30014.
RefSeqiNP_012913.3. NM_001179578.3.

Genome annotation databases

EnsemblFungiiYKL012W; YKL012W; YKL012W.
GeneIDi853857.
KEGGisce:YKL012W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S53418 Genomic DNA. Translation: AAB24902.1.
Z28012 Genomic DNA. Translation: CAA81847.1.
BK006944 Genomic DNA. Translation: DAA09144.1.
PIRiS30014.
RefSeqiNP_012913.3. NM_001179578.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1O6WNMR-A1-75[»]
2B7ENMR-A134-189[»]
2KFDNMR-A488-552[»]
ProteinModelPortaliP33203.
SMRiP33203.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34120. 144 interactors.
DIPiDIP-1620N.
IntActiP33203. 118 interactors.
MINTiMINT-386201.

PTM databases

iPTMnetiP33203.

Proteomic databases

MaxQBiP33203.
PRIDEiP33203.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYKL012W; YKL012W; YKL012W.
GeneIDi853857.
KEGGisce:YKL012W.

Organism-specific databases

EuPathDBiFungiDB:YKL012W.
SGDiS000001495. PRP40.

Phylogenomic databases

GeneTreeiENSGT00820000127014.
HOGENOMiHOG000001088.
InParanoidiP33203.
KOiK12821.
OMAiRDPRYWM.
OrthoDBiEOG092C1L62.

Enzyme and pathway databases

BioCyciYEAST:G3O-31821-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP33203.
PROiP33203.

Family and domain databases

Gene3Di1.10.10.440. 3 hits.
InterProiIPR002713. FF_domain.
IPR001202. WW_dom.
[Graphical view]
PfamiPF01846. FF. 3 hits.
PF00397. WW. 2 hits.
[Graphical view]
SMARTiSM00441. FF. 4 hits.
SM00456. WW. 2 hits.
[Graphical view]
SUPFAMiSSF51045. SSF51045. 2 hits.
SSF81698. SSF81698. 3 hits.
PROSITEiPS51676. FF. 6 hits.
PS01159. WW_DOMAIN_1. 2 hits.
PS50020. WW_DOMAIN_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPRP40_YEAST
AccessioniPrimary (citable) accession number: P33203
Secondary accession number(s): D6VXS4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: November 2, 2016
This is version 153 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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 XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: 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.