O43172 (PRP4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
U4/U6 small nuclear ribonucleoprotein Prp4

Alternative name(s):
PRP4 homolog
Short name=hPrp4
U4/U6 snRNP 60 kDa protein
WD splicing factor Prp4

Gene names

Name:	PRPF4
Synonyms:	PRP4

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	522 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in pre-mRNA splicing.
Subunit structure	Interacts directly with PRPF18, PPIH and PRPF3. Part of a heteromeric complex containing PPIH, PRPF3 and PRPF4 that is stable in the absence of RNA. This complex interacts with the U4/U5/U6 tri-snRNP complex. Ref.2 Ref.3 Ref.7
Subcellular location	Nucleus speckle By similarity. Note: Colocalizes with spliceosomal snRNPs By similarity.
Sequence similarities	Contains 7 WD repeats.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Coding sequence diversity	Alternative splicing
Domain	Repeat WD repeat
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	nuclear mRNA splicing, via spliceosome Inferred by curator. Source: BHF-UCL
Cellular component	Cajal body Inferred from direct assay. Source: BHF-UCL U4/U6 snRNP Inferred from direct assay. Source: BHF-UCL nuclear speck Inferred from electronic annotation. Source: UniProtKB-SubCell spliceosomal complex Non-traceable author statement Ref.3. Source: UniProtKB
Molecular function	protein binding Inferred from physical interaction. Source: BHF-UCL
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O43172-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: O43172-2)

The sequence of this isoform differs from the canonical sequence as follows:
     10-10: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 522

522

U4/U6 small nuclear ribonucleoprotein Prp4

PRO_0000051149

Regions

Repeat

229 – 268

40

WD 1

Repeat

271 – 318

48

WD 2

Repeat

321 – 360

40

WD 3

Repeat

363 – 402

40

WD 4

Repeat

405 – 444

40

WD 5

Repeat

447 – 487

41

WD 6

Repeat

490 – 521

32

WD 7

Amino acid modifications

Modified residue

27

1

N6-acetyllysine Ref.8

Natural variations

Alternative sequence

10

1

Missing in isoform 2.

VSP_006785

Experimental info

Sequence conflict

78 – 103

26

HISER…INVST → ISASDRQKYWLSLREGSEPG RSMFPP in AAC02261. Ref.3

Sequence conflict

78

1

H → R in AAC51925. Ref.2

Sequence conflict

86

1

V → L in AAB87640. Ref.1

Sequence conflict

134

1

R → K in AAB87640. Ref.1

Sequence conflict

141

1

G → D in AAB87640. Ref.1

Sequence conflict

176

1

Missing in AAC02261. Ref.3

Sequence conflict

275 – 282

8

NVGAIVFH → KKEQLHSI in AAC02261. Ref.3

Sequence conflict

405

1

G → D in AAB87640. Ref.1

Sequence conflict

447

1

A → P in AAB87640. Ref.1

Sequence conflict

510

1

C → Y in AAB87640. Ref.1

Sequence conflict

521

1

A → L in AAB87640. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

522

Helix Strand Turn

Details...

Helix

108 – 114

7

Beta strand

119 – 121

3

Helix

126 – 136

11

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 2, 2002. Version 2. Checksum: 08975A26D0B21857	FASTA	522	58,449
	10 20 30 40 50 60 MASSRASSTQ ATKTKAPDDL VAPVVKKPHI YYGSLEEKER ERLAKGESGI LGKDGLKAGI 70 80 90 100 110 120 EAGNINITSG EVFEIEEHIS ERQAEVLAEF ERRKRARQIN VSTDDSEVKA CLRALGEPIT 130 140 150 160 170 180 LFGEGPAERR ERLRNILSVV GTDALKKTKK DDEKSKKSKE EYQQTWYHEG PNSLKVARLW 190 200 210 220 230 240 IANYSLPRAM KRLEEARLHK EIPETTRTSQ MQELHKSLRS LNNFCSQIGD DRPISYCHFS 250 260 270 280 290 300 PNSKMLATAC WSGLCKLWSV PDCNLLHTLR GHNTNVGAIV FHPKSTVSLD PKDVNLASCA 310 320 330 340 350 360 ADGSVKLWSL DSDEPVADIE GHTVRVARVM WHPSGRFLGT TCYDRSWRLW DLEAQEEILH 370 380 390 400 410 420 QEGHSMGVYD IAFHQDGSLA GTGGLDAFGR VWDLRTGRCI MFLEGHLKEI YGINFSPNGY 430 440 450 460 470 480 HIATGSGDNT CKVWDLRQRR CVYTIPAHQN LVTGVKFEPI HGNFLLTGAY DNTAKIWTHP 490 500 510 520 GWSPLKTLAG HEGKVMGLDI SSDGQLIATC SYDRTFKLWM AE
	Isoform 2 [UniParc]. Checksum: B4EF92D9E12C9188	FASTA	521	58,321
	10 20 30 40 50 60 MASSRASSTA TKTKAPDDLV APVVKKPHIY YGSLEEKERE RLAKGESGIL GKDGLKAGIE 70 80 90 100 110 120 AGNINITSGE VFEIEEHISE RQAEVLAEFE RRKRARQINV STDDSEVKAC LRALGEPITL 130 140 150 160 170 180 FGEGPAERRE RLRNILSVVG TDALKKTKKD DEKSKKSKEE YQQTWYHEGP NSLKVARLWI 190 200 210 220 230 240 ANYSLPRAMK RLEEARLHKE IPETTRTSQM QELHKSLRSL NNFCSQIGDD RPISYCHFSP 250 260 270 280 290 300 NSKMLATACW SGLCKLWSVP DCNLLHTLRG HNTNVGAIVF HPKSTVSLDP KDVNLASCAA 310 320 330 340 350 360 DGSVKLWSLD SDEPVADIEG HTVRVARVMW HPSGRFLGTT CYDRSWRLWD LEAQEEILHQ 370 380 390 400 410 420 EGHSMGVYDI AFHQDGSLAG TGGLDAFGRV WDLRTGRCIM FLEGHLKEIY GINFSPNGYH 430 440 450 460 470 480 IATGSGDNTC KVWDLRQRRC VYTIPAHQNL VTGVKFEPIH GNFLLTGAYD NTAKIWTHPG 490 500 510 520 WSPLKTLAGH EGKVMGLDIS SDGQLIATCS YDRTFKLWMA E

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The human U4/U6 snRNP contains 60 and 90kD proteins that are structurally homologous to the yeast splicing factors Prp4p and Prp3p." Lauber J., Plessel G., Prehn S., Will C.L., Fabrizio P., Groning K., Lane W.S., Luehrmann R. RNA 3:926-941(1997) [PubMed: 9257651] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 2).
[2]	"A new cyclophilin and the human homologues of yeast Prp3 and Prp4 form a complex associated with U4/U6 snRNPs." Horowitz D.S., Kobayashi R., Krainer A.R. RNA 3:1374-1387(1997) [PubMed: 9404889] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 28-38; 58-85; 95-106; 193-200 AND 457-472, INTERACTION WITH U4/U5/U6 SNRNPS.
[3]	"Identification and characterization of human genes encoding Hprp3p and Hprp4p, interacting components of the spliceosome." Wang A., Forman-Kay J., Luo Y., Luo M., Chow Y.-H., Plumb J., Friesen J.D., Tsui L.-C., Heng H.H.Q., Woolford J.L. Jr., Hu J. Hum. Mol. Genet. 6:2117-2126(1997) [PubMed: 9328476] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), INTERACTION WITH PRPF3 AND U4/U5/U6 SNRNPS.
[4]	"DNA sequence and analysis of human chromosome 9." Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I. Nature 429:369-374(2004) [PubMed: 15164053] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Colon and Ovary.
[7]	"A human protein required for the second step of pre-mRNA splicing is functionally related to a yeast splicing factor." Horowitz D.S., Krainer A.R. Genes Dev. 11:139-151(1997) [PubMed: 9000057] [Abstract] Cited for: INTERACTION WITH PRPF18.
[8]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-27, MASS SPECTROMETRY.
[9]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]	"Crystal structure of a complex between human spliceosomal cyclophilin H and a U4/U6 snRNP-60K peptide." Reidt U., Wahl M.C., Fasshauer D., Horowitz D.S., Luehrmann R., Ficner R. J. Mol. Biol. 331:45-56(2003) [PubMed: 12875835] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 107-137 IN COMPLEX WITH PPIH.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF001687 Genomic DNA. Translation: AAB87640.1.
AF016369 mRNA. Translation: AAC51925.1.
U82756 mRNA. Translation: AAC02261.1.
AL449305 Genomic DNA. Translation: CAI10968.1.
CH471090 Genomic DNA. Translation: EAW87362.1.
BC001588 mRNA. Translation: AAH01588.1.
BC007424 mRNA. Translation: AAH07424.1.

IPI

IPI00150269.
IPI00218435.

RefSeq

NP_001231855.1. NM_001244926.1.
NP_004688.2. NM_004697.4.

UniGene

Hs.530284.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1MZW	X-ray	2.00	B	107-137	[»]

ProteinModelPortal

O43172.

SMR

O43172. Positions 107-137, 229-521.

ModBase

Search...

Protein-protein interaction databases

IntAct

O43172. 32 interactions.

MINT

MINT-270624.

STRING

O43172.

PTM databases

PhosphoSite

O43172.

Proteomic databases

PRIDE

O43172.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000374198; ENSP00000363313; ENSG00000136875.

GeneID

9128.

KEGG

hsa:9128.

UCSC

uc004bgx.1. human.

Organism-specific databases

CTD

9128.

GeneCards

GC09P116037.

H-InvDB

HIX0201385.

HGNC

HGNC:17349. PRPF4.

HPA

HPA021794.
HPA022248.

MIM

607795. gene.

neXtProt

NX_O43172.

PharmGKB

PA38448.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG14383.

GeneTree

ENSGT00600000084025.

HOGENOM

HBG435054.

HOVERGEN

HBG030892.

InParanoid

O43172.

OMA

EGHSKGV.

OrthoDB

EOG45DWP9.

PhylomeDB

O43172.

Enzyme and pathway databases

Reactome

REACT_1675. mRNA Processing.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

O43172.

Bgee

O43172.

CleanEx

HS_PRPF4.

Genevestigator

O43172.

GermOnline

ENSG00000136875. Homo sapiens.

Family and domain databases

InterPro

IPR020472. G-protein_beta_WD-40_rep.
IPR014906. PRP4.
IPR003648. SFM.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR011046. WD40_repeat-like_dom.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]

Gene3D

G3DSA:2.130.10.10. WD40/YVTN_repeat-like. 1 hit.

KO

K12662.

Pfam

PF08799. PRP4. 1 hit.
PF00400. WD40. 7 hits.
[Graphical view]

PRINTS

PR00320. GPROTEINBRPT.

SMART

SM00500. SFM. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]

SUPFAM

SSF50978. WD40_like. 1 hit.

PROSITE

PS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 6 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

34217.

SOURCE

Search...

Entry information

Entry name

PRP4_HUMAN

Accession

Primary (citable) accession number: O43172
Secondary accession number(s): O43445 , O43864, Q5T1M8, Q96DG2, Q96IK4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 2, 2002
Last sequence update:	May 2, 2002
Last modified:	January 25, 2012
This is version 120 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.