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Q08685 (CLP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
mRNA cleavage and polyadenylation factor CLP1
Gene names
Name:CLP1
Ordered Locus Names:YOR250C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length445 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Component of the cleavage factor IA (CF IA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation. Associates with HRB1/CF IB to form the cleavage factor I (CF I) complex. CF I is required for correct positioning of a larger protein complex, the cleavage and polyadenylation factor (CPF) complex, which contains the catalytic subunits executing mRNA cleavage and polyadenylation. CLP1 mediates interactions between CF IA and CPF factors. CLP1 is also involved in maintaining the CF IA interaction with the C-terminal domain of RNA Pol II largest subunit via PCF11, which links pre-mRNA 3'-end processing to transcription termination. Ref.7 Ref.10 Ref.11 Ref.12

Subunit structure

Component of the cleavage factor IA (CF IA) complex, which is a heterohexameric complex with 2:2:1:1 stoichiometry of RNA14, RNA15, PCF11 and CLP1. It contains 2 copies of an RNA14-RNA15 dimer and 1 copy of CLP1-PCF11. The complex interacts with the cleavage factor HRB1/CF IB to form the cleavage factor I (CF I) complex, and binds to RNA. Interacts directly with PCF11. Interacts with the CPF components CFT1, PTA1, PFS2, YSH1 and SSU72. Ref.6 Ref.9 Ref.10 Ref.11

Subcellular location

Nucleus By similarity HAMAP-Rule MF_03035.

Disruption phenotype

Causes defective 3'-end formation and transcriptional read-through. Ref.10

Sequence similarities

Belongs to the Clp1 family. Clp1 subfamily.

Caution

May lack the polyribonucleotide 5'-hydroxyl-kinase and polynucleotide 5'-hydroxyl-kinase activities that are characteristic of the human ortholog.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PCF11P3908113EBI-29732,EBI-12980

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 445445mRNA cleavage and polyadenylation factor CLP1 HAMAP-Rule MF_03035
PRO_0000076211

Regions

Nucleotide binding133 – 1386ATP HAMAP-Rule MF_03035

Sites

Binding site331ATP
Binding site721ATP; via carbonyl oxygen

Experimental info

Mutagenesis1361K → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-137. Ref.10
Mutagenesis1371T → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-136. Ref.10
Mutagenesis1611D → A: Compromises interaction with PCF11. No effect on growth. Ref.8 Ref.10

Secondary structure

................................................................................. 445
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q08685 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: B00F7659E83090DA

FASTA44550,226
        10         20         30         40         50         60 
MASLPGIDEH TTSEELITGD NEWHKLVIPK GSDWQIDLKA EGKLIVKVNS GIVEIFGTEL 

        70         80         90        100        110        120 
AVDDEYTFQN WKFPIYAVEE TELLWKCPDL TTNTITVKPN HTMKYIYNLH FMLEKIRMSN 

       130        140        150        160        170        180 
FEGPRVVIVG GSQTGKTSLS RTLCSYALKF NAYQPLYINL DPQQPIFTVP GCISATPISD 

       190        200        210        220        230        240 
ILDAQLPTWG QSLTSGATLL HNKQPMVKNF GLERINENKD LYLECISQLG QVVGQRLHLD 

       250        260        270        280        290        300 
PQVRRSGCIV DTPSISQLDE NLAELHHIIE KLNVNIMLVL CSETDPLWEK VKKTFGPELG 

       310        320        330        340        350        360 
NNNIFFIPKL DGVSAVDDVY KRSLQRTSIR EYFYGSLDTA LSPYAIGVDY EDLTIWKPSN 

       370        380        390        400        410        420 
VFDNEVGRVE LFPVTITPSN LQHAIIAITF AERRADQATV IKSPILGFAL ITEVNEKRRK 

       430        440 
LRVLLPVPGR LPSKAMILTS YRYLE 

« Hide

References

« Hide 'large scale' references
[1]"Sequencing analysis of a 36.8 kb fragment of yeast chromosome XV reveals 26 open reading frames including SEC63, CDC31, SUG2, GCD1, RBL2, PNT1, PAC1 and VPH1."
Poirey R., Jauniaux J.-C.
Yeast 13:483-487(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. expand/collapse author list , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]"Purification of the Saccharomyces cerevisiae cleavage/polyadenylation factor I. Separation into two components that are required for both cleavage and polyadenylation of mRNA 3' ends."
Kessler M.M., Zhao J., Moore C.L.
J. Biol. Chem. 271:27167-27175(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: COMPOSITION OF THE CFIA COMPLEX.
[6]"The major yeast poly(A)-binding protein is associated with cleavage factor IA and functions in premessenger RNA 3'-end formation."
Minvielle-Sebastia L., Preker P.J., Wiederkehr T., Strahm Y., Keller W.
Proc. Natl. Acad. Sci. U.S.A. 94:7897-7902(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE CFIA COMPLEX.
[7]"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.
[8]"Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in vivo."
Ramirez A., Shuman S., Schwer B.
RNA 14:1737-1745(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: LACK OF POLYNUCLEOTIDE KINASE ACTIVITY, MUTAGENESIS OF 136-LYS-THR-137 AND ASP-161.
[9]"Reconstitution of CF IA from overexpressed subunits reveals stoichiometry and provides insights into molecular topology."
Gordon J.M., Shikov S., Kuehner J.N., Liriano M., Lee E., Stafford W., Poulsen M.B., Harrison C., Moore C., Bohm A.
Biochemistry 50:10203-10214(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT.
[10]"The P-loop domain of yeast Clp1 mediates interactions between CF IA and CPF factors in pre-mRNA 3' end formation."
Holbein S., Scola S., Loll B., Dichtl B.S., Hubner W., Meinhart A., Dichtl B.
PLoS ONE 6:E29139-E29139(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBUNIT, DISRUPTION PHENOTYPE, MUTAGENESIS OF LYS-136; THR-137 AND ASP-161.
[11]"The interaction of Pcf11 and Clp1 is needed for mRNA 3'-end formation and is modulated by amino acids in the ATP-binding site."
Ghazy M.A., Gordon J.M., Lee S.D., Singh B.N., Bohm A., Hampsey M., Moore C.
Nucleic Acids Res. 40:1214-1225(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH PCF11.
[12]"An essential role for Clp1 in assembly of polyadenylation complex CF IA and Pol II transcription termination."
Haddad R., Maurice F., Viphakone N., Voisinet-Hakil F., Fribourg S., Minvielle-Sebastia L.
Nucleic Acids Res. 40:1226-1239(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[13]"Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor."
Noble C.G., Beuth B., Taylor I.A.
Nucleic Acids Res. 35:87-99(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF 2-445 IN COMPLEX WITH ATP AND PCF11.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z75158 Genomic DNA. Translation: CAA99472.1.
AY558048 Genomic DNA. Translation: AAS56374.1.
BK006948 Genomic DNA. Translation: DAA11017.1.
PIRS67147.
RefSeqNP_014893.1. NM_001183669.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2NPIX-ray2.95A/B2-445[»]
4C0BX-ray2.77A/B1-445[»]
4C0HX-ray2.70A/B1-445[»]
4OI4X-ray2.40A/C1-445[»]
ProteinModelPortalQ08685.
SMRQ08685. Positions 19-445.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34640. 35 interactions.
DIPDIP-1487N.
IntActQ08685. 9 interactions.
MINTMINT-394953.
STRING4932.YOR250C.

Proteomic databases

MaxQBQ08685.
PaxDbQ08685.
PeptideAtlasQ08685.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOR250C; YOR250C; YOR250C.
GeneID854424.
KEGGsce:YOR250C.

Organism-specific databases

CYGDYOR250c.
SGDS000005776. CLP1.

Phylogenomic databases

eggNOGCOG5623.
GeneTreeENSGT00390000000344.
HOGENOMHOG000231935.
KOK14399.
OMAWHGCELE.
OrthoDBEOG789CM7.

Enzyme and pathway databases

BioCycYEAST:G3O-33742-MONOMER.

Gene expression databases

GenevestigatorQ08685.

Family and domain databases

HAMAPMF_03035. Clp1.
InterProIPR028606. Clp1.
IPR029007. MobB-typ_P-loop.
IPR027417. P-loop_NTPase.
IPR010655. Pre-mRNA_cleavage_cplxII_Clp1.
[Graphical view]
PfamPF06807. Clp1. 1 hit.
PF03205. MobB. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 2 hits.
ProtoNetSearch...

Other

EvolutionaryTraceQ08685.
NextBio976637.
PROQ08685.

Entry information

Entry nameCLP1_YEAST
AccessionPrimary (citable) accession number: Q08685
Secondary accession number(s): D6W2V1
Entry history
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: November 1, 1996
Last modified: July 9, 2014
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XV

Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references