P39081 (PCF11_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein PCF11

Alternative name(s):
protein 1 of CF I

Gene names

Name:	PCF11
Ordered Locus Names:	YDR228C
ORF Names:	YD9934.13C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	626 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the cleavage factor IA (CFIA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factor NAB4/CFIB and the cleavage and polyadenylation factor (CPF) complex. Independently involved in RNA polymerase II transcript termination. Binds RNA. Seems to bridge RNA polymerase II and the native transcript and may be involved in dismantling the RNA polymerase II elongation complex. Ref.5 Ref.10
Subunit structure	Component of the CFIA complex, which is composed of RNA14, RNA15, PCF11 and CLP1. Interacts with RNA14, RNA15 and RTT103. Interacts directly with the phosphorylated CTD domain of RPB1/RNA polymerase II. Ref.4 Ref.6 Ref.7 Ref.9
Subcellular location	Nucleus Potential.
Miscellaneous	Present with 2800 molecules/cell in log phase SD medium.
Sequence similarities	Contains 1 CID domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation Transcription termination mRNA processing
Cellular component	Nucleus
Ligand	RNA-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mRNA cleavage Inferred from direct assay Ref.5. Source: SGD mRNA polyadenylation Inferred from direct assay Ref.5. Source: SGD regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW termination of RNA polymerase II transcription Inferred from direct assay Ref.7Ref.10. Source: SGD
Cellular_component	mRNA cleavage factor complex Inferred from physical interaction Ref.5. Source: SGD
Molecular_function	RNA polymerase II core binding Inferred from direct assay Ref.7. Source: SGD mRNA binding Inferred from direct assay Ref.10. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CLP1	Q08685	13	EBI-12980,EBI-29732
RNA14	P25298	12	EBI-12980,EBI-15632
RNA15	P25299	9	EBI-12980,EBI-15640

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 626

626

Protein PCF11

PRO_0000058247

Regions

Domain

4 – 139

136

CID

Region

1 – 130

130

Interaction with RBP1 CTD (CID)

Compositional bias

234 – 253

20

Poly-Gln

Compositional bias

470 – 473

4

Poly-Thr

Experimental info

Mutagenesis

66

1

A → D: Loss of interaction with RBP1 CTD. Ref.7

Mutagenesis

68 – 70

3

DSI → AAA: Loss of interaction with RBP1 CTD. Ref.7

Sequence conflict

286 – 288

3

NSL → ILS in AAC33145. Ref.3

Sequence conflict

515

1

I → V in AAC33145. Ref.3

Secondary structure

1

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626

Helix Strand Turn

Details...

Helix

3 – 16

14

Helix

24 – 36

13

Helix

38 – 40

3

Helix

41 – 54

14

Helix

57 – 73

17

Helix

78 – 83

6

Helix

86 – 95

10

Helix

99 – 112

14

Helix

115 – 117

3

Helix

125 – 137

13

Helix

486 – 491

6

Turn

494 – 497

4

Sequences

	Sequence		Length	Mass (Da)
	P39081 [UniParc]. Last modified July 15, 1998. Version 2. Checksum: 66F91BA9577E82F1	FASTA	626	71,898
	10 20 30 40 50 60 MDHDTEVIVK DFNSILEELT FNSRPIITTL TKLAEENISC AQYFVDAIES RIEKCMPKQK 70 80 90 100 110 120 LYAFYALDSI CKNVGSPYTI YFSRNLFNLY KRTYLLVDNT TRTKLINMFK LWLNPNDTGL 130 140 150 160 170 180 PLFEGSALEK IEQFLIKASA LHQKNLQAML PTPTVPLLLR DIDKLTCLTS ERLKNQPNDE 190 200 210 220 230 240 KLKMKLLVLS QLKQELKREK LTLNALKQVQ MQLRQVFSQD QQVLQERMRY HELQQQQQQQ 250 260 270 280 290 300 QQQQQQQQQQ QQQYHETKDM VGSYTQNSNS AIPLFGNNSD TTNQQNSLSS SLFGNISGVE 310 320 330 340 350 360 SFQEIEKKKS LNKINNLYAS LKAEGLIYTP PKESIVTLYK KLNGHSNYSL DSHEKQLMKN 370 380 390 400 410 420 LPKIPLLNDI LSDCKAYFAT VNIDVLNNPS LQLSEQTLLQ ENPIVQNNLI HLLYRSKPNK 430 440 450 460 470 480 CSVCGKRFGN SESEKLLQNE HLDWHFRINT RIKGSQNTAN TGISNSNLNT TTTRKNIQSR 490 500 510 520 530 540 NWYLSDSQWA AFKDDEITST KHKNDYTDPH ANKNIDKSAL NIHADENDEG SVDNTLGSDR 550 560 570 580 590 600 SNELEIRGKY VVVPETSQDM AFKCPICKET VTGVYDEESG EWVWKNTIEV NGKYFHSTCY 610 620 HETSQNSSKS NSGKVGLDDL KKLVTK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"Insertion site specificity of the transposon Tn3." Davies C.J., Hutchison C.A. III Nucleic Acids Res. 23:507-514(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 286-626.
[4]	"PCF11 encodes a third protein component of yeast cleavage and polyadenylation factor I." Amrani N., Minet M., Wyers F., Dufour M.-E., Aggerbeck L.P., Lacroute F. Mol. Cell. Biol. 17:1102-1109(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE CFIA COMPLEX, INTERACTION WITH RNA14 AND RNA15.
[5]	"Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I." Gross S., Moore C. Proc. Natl. Acad. Sci. U.S.A. 98:6080-6085(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE CFIA COMPLEX.
[6]	"Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae." Barilla D., Lee B.A., Proudfoot N.J. Proc. Natl. Acad. Sci. U.S.A. 98:445-450(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RBP1.
[7]	"Independent functions of yeast Pcf11p in pre-mRNA 3' end processing and in transcription termination." Sadowski M., Dichtl B., Huebner W., Keller W. EMBO J. 22:2167-2177(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RBP1, MUTAGENESIS OF ALA-66 AND 68-ASP--ILE-70.
[8]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]	"The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II." Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F., Buratowski S. Nature 432:517-522(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RTT103.
[10]	"CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3'-end processing factor, Pcf11." Zhang Z., Fu J., Gilmour D.S. Genes Dev. 19:1572-1580(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, RNA-BINDING.
[11]	"Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors." Meinhart A., Cramer P. Nature 430:223-226(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-140.
[12]	"Key features of the interaction between Pcf11 CID and RNA polymerase II CTD." Noble C.G., Hollingworth D., Martin S.R., Ennis-Adeniran V., Smerdon S.J., Kelly G., Taylor I.A., Ramos A. Nat. Struct. Mol. Biol. 12:144-151(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-138.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z48612 Genomic DNA. Translation: CAA88508.1.
U13239 Genomic DNA. Translation: AAC33145.1.
BK006938 Genomic DNA. Translation: DAA12070.1.

PIR

S59435.

RefSeq

NP_010514.3. NM_001180536.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SZ9	X-ray	2.10	A/B/C	1-140	[»]
1SZA	X-ray	2.20	A/B/C	1-140	[»]
2BF0	X-ray	2.30	X	1-138	[»]
2NPI	X-ray	2.95	C/D	454-563	[»]

ProteinModelPortal

P39081.

SMR

P39081. Positions 2-140.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-944N.

IntAct

P39081. 77 interactions.

MINT

MINT-389878.

STRING

4932.YDR228C.

Proteomic databases

PaxDb

P39081.

PeptideAtlas

P39081.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDR228C; YDR228C; YDR228C.

GeneID

851814.

KEGG

sce:YDR228C.
sce:YDR233C.

Organism-specific databases

CYGD

YDR228c.

SGD

S000002636. PCF11.

Phylogenomic databases

eggNOG

NOG268273.

GeneTree

ENSGT00440000034259.

HOGENOM

HOG000115468.

KO

K14400.

OMA

DWHFRIN.

OrthoDB

EOG408RHB.

Gene expression databases

Genevestigator

P39081.

GermOnline

YDR228C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

1.25.40.90. 1 hit.

InterPro

IPR021605. CFIA_Pcf11.
IPR006569. CID_dom.
IPR008942. ENTH_VHS.
[Graphical view]

Pfam

PF11526. CFIA_Pcf11. 1 hit.
[Graphical view]

SMART

SM00582. RPR. 1 hit.
[Graphical view]

SUPFAM

SSF48464. ENTH_VHS. 1 hit.

PROSITE

PS51391. CID. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P39081.

NextBio

969674.

Entry information

Entry name

PCF11_YEAST

Accession

Primary (citable) accession number: P39081
Secondary accession number(s): D6VSL0, Q04932

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	July 15, 1998
Last modified:	May 1, 2013
This is version 109 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program