P33203 (PRP40_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pre-mRNA-processing protein PRP40

Gene names

Name:	PRP40
Ordered Locus Names:	YKL012W
ORF Names:	YKL165

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	583 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.6 Ref.7 Ref.8
Subunit structure	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. Ref.6 Ref.7 Ref.8
Subcellular location	Nucleus Ref.8.
Domain	The WW and FF domains bind to the phosphorylated carboxy-terminal domain of RPB1.
Sequence similarities	Belongs to the PRPF40 family. Contains 4 FF domains. Contains 2 WW domains.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus
Domain	Repeat
Molecular function	Ribonucleoprotein
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	nuclear mRNA splicing, via spliceosome Inferred from direct assay Ref.5. Source: SGD
Cellular component	U1 snRNP Inferred from direct assay. Source: SGD U2-type prespliceosome Inferred from direct assay. Source: SGD
Molecular function	RNA binding Inferred from direct assay Ref.5. Source: SGD protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ADE12	P80210	2	EBI-701,EBI-14267
AMD1	P15274	2	EBI-701,EBI-2548
FMP40	Q08968	2	EBI-701,EBI-29375
GPH1	P06738	2	EBI-701,EBI-13389
LHP1	P33399	2	EBI-701,EBI-10046
MLS1	P30952	2	EBI-701,EBI-10428
NPT1	P39683	2	EBI-701,EBI-12218
PCK1	P10963	2	EBI-701,EBI-13770
SNU71	P53207	5	EBI-701,EBI-736
STM1	P39015	2	EBI-701,EBI-11238
YDL086W	Q07505	2	EBI-701,EBI-5951
YJR096W	P47137	2	EBI-701,EBI-25572

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 583

583

Pre-mRNA-processing protein PRP40

PRO_0000076084

Regions

Domain

1 – 31

31

WW 1

Domain

42 – 72

31

WW 2

Domain

134 – 185

52

FF 1

Domain

203 – 254

52

FF 2

Domain

357 – 410

54

FF 3

Domain

494 – 549

56

FF 4

Amino acid modifications

Modified residue

576

1

Phosphothreonine Ref.9

Modified residue

583

1

Phosphotyrosine Ref.9

Experimental info

Mutagenesis

240

1

S → P in PRP40-1 suppressor; affects SAR1 mRNA accumulation in U1-U4 mutant at 18 degrees Celsius. Ref.5

Mutagenesis

274

1

L → A: Temperature sensitive growth at 36 degrees Celsius. Ref.8

Mutagenesis

277

1

L → A: Temperature sensitive growth at 36 degrees Celsius. Ref.8

Mutagenesis

281

1

L → A: Temperature sensitive growth at 36 degrees Celsius. Ref.8

Mutagenesis

340

1

L → A: Wild-type growth at 36 degrees Celsius. Ref.8

Mutagenesis

344

1

L → A: Wild-type growth at 36 degrees Celsius. Ref.8

Mutagenesis

347

1

L → I: Wild-type growth at 36 degrees Celsius. Ref.8

Secondary structure

1

.

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583

Helix Strand Turn

Details...

Beta strand

4 – 8

5

Beta strand

14 – 18

5

Turn

19 – 22

4

Beta strand

23 – 27

5

Helix

30 – 43

14

Beta strand

46 – 49

4

Beta strand

55 – 59

5

Turn

60 – 63

4

Beta strand

64 – 68

5

Helix

134 – 145

12

Helix

154 – 164

11

Helix

167 – 170

4

Helix

175 – 187

13

Sequences

	Sequence		Length	Mass (Da)
	P33203 [UniParc]. Last modified February 1, 1994. Version 1. Checksum: BA1C1C91D532524C	FASTA	583	69,065
	10 20 30 40 50 60 MSIWKEAKDA SGRIYYYNTL TKKSTWEKPK ELISQEELLL RENGWKAAKT ADGKVYYYNP 70 80 90 100 110 120 TTRETSWTIP AFEKKVEPIA EQKHDTVSHA QVNGNRIALT AGEKQEPGRT INEEESQYAN 130 140 150 160 170 180 NSKLLNVRRR TKEEAEKEFI TMLKENQVDS TWSFSRIISE LGTRDPRYWM VDDDPLWKKE 190 200 210 220 230 240 MFEKYLSNRS ADQLLKEHNE TSKFKEAFQK MLQNNSHIKY YTRWPTAKRL IADEPIYKHS 250 260 270 280 290 300 VVNEKTKRQT FQDYIDTLID TQKESKKKLK TQALKELREY LNGIITTSSS ETFITWQQLL 310 320 330 340 350 360 NHYVFDKSKR YMANRHFKVL THEDVLNEYL KIVNTIENDL QNKLNELRLR NYTRDRIARD 370 380 390 400 410 420 NFKSLLREVP IKIKANTRWS DIYPHIKSDP RFLHMLGRNG SSCLDLFLDF VDEQRMYIFA 430 440 450 460 470 480 QRSIAQQTLI DQNFEWNDAD SDEITKQNIE KVLENDRKFD KVDKEDISLI VDGLIKQRNE 490 500 510 520 530 540 KIQQKLQNER RILEQKKHYF WLLLQRTYTK TGKPKPSTWD LASKELGESL EYKALGDEDN 550 560 570 580 IRRQIFEDFK PESSAPTAES ATANLTLTAS KKRHLTPAVE LDY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The sequence of a 9.3 kb segment located on the left arm of the yeast chromosome XI reveals five open reading frames including the CCE1 gene and putative products related to MYO2 and to the ribosomal protein L10." Pascolo S., Ghazvini M., Boyer J., Colleaux L., Thierry A., Dujon B. Yeast 8:987-995(1992) [PubMed: 1481574] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Complete DNA sequence of yeast chromosome XI." Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W. Nature 369:371-378(1994) [PubMed: 8196765] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry." Neubauer G., Gottschalk A., Fabrizio P., Seraphin B., Luehrmann R., Mann M. Proc. Natl. Acad. Sci. U.S.A. 94:385-390(1997) [PubMed: 9012791] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE.
[5]	"Identification of Prp40, a novel essential yeast splicing factor associated with the U1 small nuclear ribonucleoprotein particle." Kao H.-Y., Siliciano P.G. Mol. Cell. Biol. 16:960-967(1996) [PubMed: 8622699] [Abstract] Cited for: IDENTIFICATION, MUTAGENESIS OF SER-240.
[6]	"Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals." Abovich N., Rosbash M. Cell 89:403-412(1997) [PubMed: 9150140] [Abstract] Cited for: FUNCTION, INTERACTION WITH MSL5; MUD2 AND PRP8.
[7]	"The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II." Morris D.P., Greenleaf A.L. J. Biol. Chem. 275:39935-39943(2000) [PubMed: 10978320] [Abstract] Cited for: FUNCTION, INTERACTION WITH RPB1.
[8]	"The yeast splicing factor Prp40p contains functional leucine-rich nuclear export signals that are essential for splicing." Murphy M.W., Olson B.L., Siliciano P.G. Genetics 166:53-65(2004) [PubMed: 15020406] [Abstract] Cited for: FUNCTION, INTERACTION WITH CRM1, SUBCELLULAR LOCATION, MUTAGENESIS OF LEU-274; LEU-277; LEU-281; LEU-340; LEU-344 AND LEU-347.
[9]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-576 AND TYR-583, MASS SPECTROMETRY.
[10]	"Solution structure and ligand recognition of the WW domain pair of the yeast splicing factor Prp40." Wiesner S., Stier G., Sattler M., Macias M.J. J. Mol. Biol. 324:807-822(2002) [PubMed: 12460579] [Abstract] Cited for: STRUCTURE BY NMR OF 1-75.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

S53418 Genomic DNA. Translation: AAB24902.1.
Z28012 Genomic DNA. Translation: CAA81847.1.
BK006944 Genomic DNA. Translation: DAA09144.1.

PIR

S30014.

RefSeq

NP_012913.1. NM_001179578.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1O6W	NMR	-	A	1-75	[»]
2B7E	NMR	-	A	134-189	[»]
2KFD	NMR	-	A	488-552	[»]

ProteinModelPortal

P33203.

SMR

P33203. Positions 1-75, 134-189, 202-257, 348-420, 488-552.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1620N.

IntAct

P33203. 120 interactions.

MINT

MINT-386201.

STRING

P33203.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YKL012W; YKL012W; YKL012W.

GeneID

853857.

KEGG

sce:YKL012W.

NMPDR

fig|4932.3.peg.3899.

Organism-specific databases

CYGD

YKL012w.

SGD

S000001495. PRP40.

Phylogenomic databases

eggNOG

fuNOG07125.

GeneTree

EFGT00050000000434.

HOGENOM

HBG202347.

OMA

DDDPLWK.

OrthoDB

EOG41VPBS.

Gene expression databases

ArrayExpress

P33203.

Genevestigator

P33203.

GermOnline

YKL012W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR002713. FF_domain.
IPR001202. WW_Rsp5_WWP.
[Graphical view]

Gene3D

G3DSA:1.10.10.440. FF. 3 hits.
G3DSA:2.20.70.10. G3DSA:2.20.70.10. 2 hits.

KO

K12821.

Pfam

PF01846. FF. 4 hits.
PF00397. WW. 2 hits.
[Graphical view]

SMART

SM00441. FF. 4 hits.
SM00456. WW. 2 hits.
[Graphical view]

SUPFAM

SSF81698. FF. 3 hits.
SSF51045. WW_Rsp5_WWP. 2 hits.

PROSITE

PS01159. WW_DOMAIN_1. 2 hits.
PS50020. WW_DOMAIN_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

NextBio

975100.

Entry information

Entry name

PRP40_YEAST

Accession

Primary (citable) accession number: P33203
Secondary accession number(s): D6VXS4

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	February 1, 1994
Last modified:	December 14, 2011
This is version 112 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program