Protein Overview: PRP40

General Information:
Name(s) found:	PRP40 / YKL012W [SGD]
Description(s) found: SHOW ONLY BEST	gi\|6322840\|ref\|NP_012913.1\| U1 snRNP protein involved in splicing, interacts with the branchpoint-binding protein during the formation of the second commitment complex; Prp40p [Saccharomyces cerevisiae] [NCBI NR] gi\|485997\|emb\|CAA81847.1\| PRP40 [Saccharomyces cerevisiae] [NCBI NR] gi\|465672\|sp\|P33203.1\|PRP40_YEAST RecName: Full=Pre-mRNA-processing protein PRP40 [NCBI NR] pir\|\|S30014 hypothetical protein YKL012w - yeast (Saccharomyces cerevisiae) [NCBI NR] gi\|263498\|gb\|AAB24902.1\| MYO2 homolog [Saccharomyces cerevisiae] [NCBI NR] Pre-mRNA-processing protein PRP40 OS=Saccharomyces cerevisiae GN=PRP40 PE=1 SV=1 [Swiss-Prot] (P33203) Pre-mRNA processing protein PRP40 [Swiss-Prot] PRP40 Splicing factor [mips] U1 snRNP protein involved in splicing, interacts with the branchpoint-binding protein during the formation of the second commitment complex [SGD] PRP40, Chr XI from 417948-419699 [yeast_orfs2] Chr XI from 417948-419699 [yeastorf3.fasta] PRP40 SGDID:S0001495, Chr XI from 417953-419704, Verified ORF [yeastflysequest.fasta] Prp40p [Saccharomyces cerevisiae]gi\|485997\|emb\|CAA81847.1\| PRP40 [Saccharomyces cerevisiae]gi\|320761\|pir\|\|S30014 hypothetical protein YKL012w - yeast (Saccharomyces cerevisiae)gi\|263498\|gb\|AAB24902.1\| MYO2 homolog [Saccharomyces cerevisiae]gi\|465672\|s [nrdb_11152004_Chlamydomonas] PRP40 SGDID:S000001495, Chr XI from 417953-419704, Verified ORF, "U1 snRNP protein involved in splicing, interacts with the branchpoint-binding protein during the formation of the second commitment complex" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] PRP40 [Saccharomyces cerevisiae] [nr-271106-contam.fasta] MYO2 homolog [Saccharomyces cerevisiae] [nr-271106-contam.fasta] U1 snRNP protein involved in splicing, interacts with the branchpoint-binding protein during the formation of the second commitment complex; Prp40p [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Pre-mRNA-processing protein PRP40 [nr-271106-contam.fasta] [chemostatdb.fasta] Pre-mRNA-processing protein PRP40 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PRP40 PE=1 SV=1 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta] PRP40 SGDID:S000001495, Chr XI from 418310-420061, Genome Release 64-1-1, Verified ORF, "U1 snRNP protein involved in splicing, interacts with the branchpoint-binding protein during the formation of the second commitment complex" [yeast-030211-contam.fasta] PRP40 SGDID:S000001495, Chr XI from 418310-420061, Genome Release 64-2-1, Verified ORF, "U1 snRNP protein involved in splicing; interacts with the branchpoint-binding protein during the formation of the second commitment complex" [20141208_orf_trans.fasta] YKL012W SGDID:S000001495, Chr XI from 418310-420061, Genome Release 64-1-1, Verified ORF, "U1 snRNP protein involved in splicing, interacts with the branchpoint-binding protein during the formation of the second commitment complex" [2016-01-SGD_Yeast_Contam_Riffle_20140507-Ska-Hec-110-tubulin.fasta]
Organism:	Saccharomyces cerevisiae
Length:	583 amino acids
Gene Ontology:
Cellular Component:	U1 snRNP [IDA ]
Biological Process:	nuclear mRNA splicing, via spliceosome [IDA]
Molecular Function:	RNA binding [IDA]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSIWKEAKDA SGRIYYYNTL TKKSTWEKPK ELISQEELLL RENGWKAAKT ADGKVYYYNP  60
   61 TTRETSWTIP AFEKKVEPIA EQKHDTVSHA QVNGNRIALT AGEKQEPGRT INEEESQYAN 120
  121 NSKLLNVRRR TKEEAEKEFI TMLKENQVDS TWSFSRIISE LGTRDPRYWM VDDDPLWKKE 180
  181 MFEKYLSNRS ADQLLKEHNE TSKFKEAFQK MLQNNSHIKY YTRWPTAKRL IADEPIYKHS 240
  241 VVNEKTKRQT FQDYIDTLID TQKESKKKLK TQALKELREY LNGIITTSSS ETFITWQQLL 300
  301 NHYVFDKSKR YMANRHFKVL THEDVLNEYL KIVNTIENDL QNKLNELRLR NYTRDRIARD 360
  361 NFKSLLREVP IKIKANTRWS DIYPHIKSDP RFLHMLGRNG SSCLDLFLDF VDEQRMYIFA 420
  421 QRSIAQQTLI DQNFEWNDAD SDEITKQNIE KVLENDRKFD KVDKEDISLI VDGLIKQRNE 480
  481 KIQQKLQNER RILEQKKHYF WLLLQRTYTK TGKPKPSTWD LASKELGESL EYKALGDEDN 540
  541 IRRQIFEDFK PESSAPTAES ATANLTLTAS KKRHLTPAVE LDY

Protein Complex Data

	PUBLICATION	TOPOLOGY	COCOMPLEXED PROTEINS
View Details	Riffle et al. (2010) (Unpublished Data)		BRR1 BRR2 CBC2 CSN12 CUS1 DIB1 HSH155 LEA1 LUC7 MUD1 NAM8 PRP39 PRP4 PRP40 PRP42 PRP6 PRP8 RSE1 SMB1 SMD1 SMD2 SMD3 SME1 SMX3 SNP1 SNU114 SNU56 SNU66 SNU71 STO1 YHC1
View Details	(MIPS) Mewes HW, et al. (2004)		AAR2 BRR1 BRR2 CBC2 CDC40 CWC15 CWC2 CWC22 CWC23 DHR2 LSM4 MAK5 MUD2 PRP16 PRP18 PRP2 PRP22 PRP24 PRP28 PRP31 PRP38 PRP39 PRP4 PRP40 PRP43 PRP5 PRP6 PRP8 SLU7 SMD1 SMD3 SME1 SNP1 SPP2 SPP381 STO1 YHC1
View Details	Krogan NJ, et al. (2006)		AAR2 BRR1 BRR2 CSE1 LUC7 MUD1 NAM8 PRP2 PRP3 PRP31 PRP39 PRP40 PRP42 PRP6 PRP8 RRG7 SMB1 SMD1 SMD2 SMD3 SME1 SMX2 SMX3 SNP1 SNU114 SNU56 SNU66 SNU71 TAD2 YDL085C-A YHC1 YJU2 YNL092W
View Details	Gavin AC, et al. (2006)		LUC7 MUD1 NAM8 PRP39 PRP40 PRP42 SNP1 SNU56 SNU71 YHC1
View Details	Gavin AC, et al. (2002)		AAR2 AIR2 BRR1 BUD31 BUR2 CBC2 CDC33 CEF1 CLF1 CSN12 CUS1 CWC2 CWC22 CWC23 DHH1 DIB1 ECM2 GCN2 HRT1 HSH155 HSH49 HTA1 IMG1 KAP95 LEA1 LIN1 LSM1 LSM2 LSM4 LSM5 LSM6 LSM7 LUC7 MRP7 MRPL28 MRPL3 MRPL35 MRPL38 MRPL4 MRPL8 MRPS5 MSH4 MSL1 MUD1 NAB3 NAB6 NAM8 NPL3 NRD1 NUP60 PAT1 PRP11 PRP18 PRP19 PRP21 PRP24 PRP28 PRP3 PRP31 PRP38 PRP39 PRP4 PRP40 PRP42 PRP43 PRP46 PRP6 PRP8 PRP9 RSE1 RVB2 SCP160 SEN1 SGV1 SLU7 SMB1 SMD1 SMD2 SMD3 SME1 SMX2 SMX3 SNP1 SNT309 SNU114 SNU23 SNU56 SNU66 SNU71 SPP381 SPP382 SRB2 SRO9 SRP1 STO1 SYF1 THO2 TIF4631 TIF4632 TOS4 UTP21 YEF3 YML6 YRA2
View Details	Ho Y, et al. (2002)		CKA1 CKA2 CKB1 CKB2 DIP2 ESL2 KRE33 LCP5 NAN1 NOP1 NOP56 PNO1 PRP40 PTC5 PWP2 RRP5 TFP1 UTP10 UTP11 UTP13 UTP14 UTP18 UTP21 UTP22 UTP30 UTP6
View Details	Qiu et al. (2008)		AAR2 BRR1 BRR2 CBC2 CDC40 CEF1 CLF1 CUS1 CUS2 CWC15 CWC2 CWC21 CWC22 CWC23 DHR2 DIB1 ECM2 HSH155 HSH49 IST3 ISY1 LEA1 LSM2 LSM3 LSM4 LSM6 LSM8 LUC7 MAK5 MSL1 MUD1 MUD2 NAM8 NTC20 PRP11 PRP16 PRP18 PRP19 PRP2 PRP21 PRP22 PRP24 PRP28 PRP3 PRP31 PRP38 PRP39 PRP4 PRP40 PRP42 PRP43 PRP45 PRP46 PRP5 PRP6 PRP8 PRP9 RSE1 SLU7 SMB1 SMD1 SMD2 SMD3 SME1 SMX2 SMX3 SNP1 SNT309 SNU114 SNU23 SNU56 SNU66 SNU71 SPP2 SPP381 SPP382 STO1 SUB2 SYF1 SYF2 YHC1

Mass Spectrometry Data

The following runs contain data for this protein:

	BAIT	COMMENTS	PUBLICATION
View Run	MLP2	#04 Alpha Factor Prep2	Keck JM, et al. (2011)
View Run	MLP2	#12 Mitotic Prep1-TiO2 Flowthrough	Keck JM, et al. (2011)

Yeast Two-Hybrid Data

The following interactions contain this protein:

NOT SHOWING SINGLE HITS. [ Show Single Hits ]

[View our yeast two-hybrid interpretation guidelines.]

	BAIT	PREY	HITS	PUBLICATION
View Screen	PRP40	SIP2	2	Unpublished Fields Lab Data
View Screen	SPP382	PRP40	2	Hazbun TR, et al. (2003)
View Screen	PRP40	SNU71	2	Unpublished Fields Lab Data
View Screen	PRP40	BNR1	2	Unpublished Fields Lab Data
View Screen	PRP40	PAN1	2	Unpublished Fields Lab Data
View Screen	THP2	PRP40	2	Unpublished Fields Lab Data
View Screen	SNX4	PRP40	2	Unpublished Fields Lab Data
View Screen	PRP40	RNP1	2	Unpublished Fields Lab Data
View Screen	PRP40	VRP1	2	Unpublished Fields Lab Data
View Screen	PRP40	LUC7	2	Unpublished Fields Lab Data
View Screen	PRP40	ADA2	2	Unpublished Fields Lab Data
View Screen	PRP40	SLG1	2	Unpublished Fields Lab Data
View Screen	PRP40	SNU71	2	Unpublished Fields Lab Data
View Screen	PRP40	HSM3	2	Unpublished Fields Lab Data
View Screen	PRP40	BNR1	2	Unpublished Fields Lab Data
View Screen	PRP40	LAS17	2	Unpublished Fields Lab Data
View Screen	PRP40	RVS167	2	Unpublished Fields Lab Data
View Screen	PRP40	MCA1	2	Unpublished Fields Lab Data
View Screen	PRP40	ACT1	2	Unpublished Fields Lab Data

Microscopy / Localization Data

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	PROTEIN(S)	PUBLICATION
View Data	PRP40	Huh WK, et al. (2003)

Protein Structure Data

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[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..33]	PSI-BLAST	27.31133	Formin binding protein FBP28 domain
2	View Details	[34..82]	PSI-BLAST	8.30103	Ubiquitin ligase NEDD4 WWIII domain
3	View Details	[83..153]	deduced	N/A	No confident structure predictions are available.
4	View Details	[154..494]	PSI-BLAST	23.69897	Heavy meromyosin subfragment
5	View Details	[495..583]	Pfam	11.537602	FF domain No confident structure predictions are available.

Functions predicted (by domain):

Gene Ontology predictions

Term	Confidence	Notes
transcription regulator activity	2.16402927467227	bayes_pls_golite062009
binding	2.02935060794966	bayes_pls_golite062009
transcription cofactor activity	1.56045209816163	bayes_pls_golite062009
transcription coactivator activity	1.54071619149498	bayes_pls_golite062009
transcription activator activity	1.50941346594353	bayes_pls_golite062009
transcription factor binding	1.46474521462806	bayes_pls_golite062009
protein binding	0.772594643545448	bayes_pls_golite062009
catalytic activity	0.210712504691113	bayes_pls_golite062009

No functions predicted.

Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

Philius Transmembrane Prediction:

Protein predicted to be:	GLOBULAR (No transmembrane regions or signal peptide)
Confidence of classification:	0.99

Source: Reynolds et al. (2008)

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2