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Q08685

- CLP1_YEAST

UniProt

Q08685 - CLP1_YEAST

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Protein

mRNA cleavage and polyadenylation factor CLP1

Gene
CLP1, YOR250C
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.4 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei33 – 331ATP
Binding sitei72 – 721ATP; via carbonyl oxygen

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi133 – 1386ATPUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. protein binding Source: IntAct

GO - Biological processi

  1. mRNA 3'-end processing Source: SGD
  2. mRNA cleavage Source: SGD
  3. mRNA polyadenylation Source: SGD
Complete GO annotation...

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33742-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
mRNA cleavage and polyadenylation factor CLP1
Gene namesi
Name:CLP1
Ordered Locus Names:YOR250C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XV

Organism-specific databases

CYGDiYOR250c.
SGDiS000005776. CLP1.

Subcellular locationi

Nucleus By similarity UniRule annotation

GO - Cellular componenti

  1. mRNA cleavage factor complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Causes defective 3'-end formation and transcriptional read-through.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi136 – 1361K → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-137. 1 Publication
Mutagenesisi137 – 1371T → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-136. 1 Publication
Mutagenesisi161 – 1611D → A: Compromises interaction with PCF11. No effect on growth. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 445445mRNA cleavage and polyadenylation factor CLP1UniRule annotationPRO_0000076211Add
BLAST

Proteomic databases

MaxQBiQ08685.
PaxDbiQ08685.
PeptideAtlasiQ08685.

Expressioni

Gene expression databases

GenevestigatoriQ08685.

Interactioni

Subunit structurei

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 SSU72.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PCF11P3908113EBI-29732,EBI-12980

Protein-protein interaction databases

BioGridi34640. 35 interactions.
DIPiDIP-1487N.
IntActiQ08685. 9 interactions.
MINTiMINT-394953.
STRINGi4932.YOR250C.

Structurei

Secondary structure

1
445
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi24 – 285
Beta strandi32 – 376
Beta strandi43 – 519
Beta strandi53 – 553
Beta strandi65 – 706
Beta strandi72 – 798
Beta strandi81 – 866
Turni92 – 943
Beta strandi96 – 994
Helixi103 – 11917
Beta strandi120 – 1223
Beta strandi125 – 1317
Helixi136 – 14712
Helixi148 – 1514
Beta strandi156 – 1594
Beta strandi166 – 1683
Beta strandi172 – 1776
Beta strandi194 – 1963
Beta strandi206 – 2094
Beta strandi212 – 2143
Helixi215 – 2173
Helixi219 – 23921
Helixi241 – 2466
Beta strandi248 – 2514
Helixi255 – 2573
Helixi263 – 2719
Beta strandi276 – 2816
Helixi286 – 29914
Helixi301 – 3033
Beta strandi304 – 3074
Helixi318 – 33417
Turni337 – 3393
Beta strandi344 – 3496
Helixi350 – 3523
Beta strandi355 – 3584
Helixi361 – 3644
Beta strandi371 – 3733
Helixi378 – 3814
Beta strandi384 – 3929
Helixi397 – 4026
Beta strandi405 – 41511
Turni416 – 4194
Beta strandi420 – 43011
Beta strandi434 – 4429

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NPIX-ray2.95A/B2-445[»]
4C0BX-ray2.77A/B1-445[»]
4C0HX-ray2.70A/B1-445[»]
4OI4X-ray2.40A/C1-445[»]
ProteinModelPortaliQ08685.
SMRiQ08685. Positions 19-445.

Miscellaneous databases

EvolutionaryTraceiQ08685.

Family & Domainsi

Sequence similaritiesi

Belongs to the Clp1 family. Clp1 subfamily.

Phylogenomic databases

eggNOGiCOG5623.
GeneTreeiENSGT00390000000344.
HOGENOMiHOG000231935.
KOiK14399.
OMAiWHGCELE.
OrthoDBiEOG789CM7.

Family and domain databases

HAMAPiMF_03035. Clp1.
InterProiIPR028606. Clp1.
IPR029007. MobB-typ_P-loop.
IPR027417. P-loop_NTPase.
IPR010655. Pre-mRNA_cleavage_cplxII_Clp1.
[Graphical view]
PfamiPF06807. Clp1. 1 hit.
PF03205. MobB. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.

Sequencei

Sequence statusi: Complete.

Q08685-1 [UniParc]FASTAAdd to Basket

« Hide

MASLPGIDEH TTSEELITGD NEWHKLVIPK GSDWQIDLKA EGKLIVKVNS    50
GIVEIFGTEL AVDDEYTFQN WKFPIYAVEE TELLWKCPDL TTNTITVKPN 100
HTMKYIYNLH FMLEKIRMSN FEGPRVVIVG GSQTGKTSLS RTLCSYALKF 150
NAYQPLYINL DPQQPIFTVP GCISATPISD ILDAQLPTWG QSLTSGATLL 200
HNKQPMVKNF GLERINENKD LYLECISQLG QVVGQRLHLD PQVRRSGCIV 250
DTPSISQLDE NLAELHHIIE KLNVNIMLVL CSETDPLWEK VKKTFGPELG 300
NNNIFFIPKL DGVSAVDDVY KRSLQRTSIR EYFYGSLDTA LSPYAIGVDY 350
EDLTIWKPSN VFDNEVGRVE LFPVTITPSN LQHAIIAITF AERRADQATV 400
IKSPILGFAL ITEVNEKRRK LRVLLPVPGR LPSKAMILTS YRYLE 445
Length:445
Mass (Da):50,226
Last modified:November 1, 1996 - v1
Checksum:iB00F7659E83090DA
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z75158 Genomic DNA. Translation: CAA99472.1.
AY558048 Genomic DNA. Translation: AAS56374.1.
BK006948 Genomic DNA. Translation: DAA11017.1.
PIRiS67147.
RefSeqiNP_014893.1. NM_001183669.1.

Genome annotation databases

EnsemblFungiiYOR250C; YOR250C; YOR250C.
GeneIDi854424.
KEGGisce:YOR250C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z75158 Genomic DNA. Translation: CAA99472.1 .
AY558048 Genomic DNA. Translation: AAS56374.1 .
BK006948 Genomic DNA. Translation: DAA11017.1 .
PIRi S67147.
RefSeqi NP_014893.1. NM_001183669.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2NPI X-ray 2.95 A/B 2-445 [» ]
4C0B X-ray 2.77 A/B 1-445 [» ]
4C0H X-ray 2.70 A/B 1-445 [» ]
4OI4 X-ray 2.40 A/C 1-445 [» ]
ProteinModelPortali Q08685.
SMRi Q08685. Positions 19-445.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34640. 35 interactions.
DIPi DIP-1487N.
IntActi Q08685. 9 interactions.
MINTi MINT-394953.
STRINGi 4932.YOR250C.

Proteomic databases

MaxQBi Q08685.
PaxDbi Q08685.
PeptideAtlasi Q08685.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YOR250C ; YOR250C ; YOR250C .
GeneIDi 854424.
KEGGi sce:YOR250C.

Organism-specific databases

CYGDi YOR250c.
SGDi S000005776. CLP1.

Phylogenomic databases

eggNOGi COG5623.
GeneTreei ENSGT00390000000344.
HOGENOMi HOG000231935.
KOi K14399.
OMAi WHGCELE.
OrthoDBi EOG789CM7.

Enzyme and pathway databases

BioCyci YEAST:G3O-33742-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q08685.
NextBioi 976637.
PROi Q08685.

Gene expression databases

Genevestigatori Q08685.

Family and domain databases

HAMAPi MF_03035. Clp1.
InterProi IPR028606. Clp1.
IPR029007. MobB-typ_P-loop.
IPR027417. P-loop_NTPase.
IPR010655. Pre-mRNA_cleavage_cplxII_Clp1.
[Graphical view ]
Pfami PF06807. Clp1. 1 hit.
PF03205. MobB. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 2 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. 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.

Entry informationi

Entry nameiCLP1_YEAST
AccessioniPrimary (citable) accession number: Q08685
Secondary accession number(s): D6W2V1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: November 1, 1996
Last modified: September 3, 2014
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Caution

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

External Data

Dasty 3

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