mRNA cleavage and polyadenylation factor CLP1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Contribute

Send feedback

Read comments (?) or add your own

Q08685 (CLP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 92. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
mRNA cleavage and polyadenylation factor CLP1

Gene names

Name:	CLP1
Ordered Locus Names:	YOR250C

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	445 AA.
Sequence status	Complete.
Protein existence	Evidence 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 a 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.

Ontologies

Keywords
Biological process	mRNA processing
Cellular component	Nucleus
Ligand	ATP-binding Nucleotide-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mRNA cleavage Inferred from direct assay Ref.7. Source: SGD mRNA polyadenylation Inferred from direct assay Ref.7. Source: SGD
Cellular_component	mRNA cleavage factor complex Inferred from physical interaction Ref.7. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PCF11	P39081	13	EBI-29732,EBI-12980

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 445

445

mRNA cleavage and polyadenylation factor CLP1 HAMAP-Rule MF_03035

PRO_0000076211

Regions

Nucleotide binding

133 – 138

ATP HAMAP-Rule MF_03035

Sites

Binding site

ATP

Binding site

ATP; via carbonyl oxygen

Experimental info

Mutagenesis

136

K → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-137. Ref.10

Mutagenesis

137

T → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-136. Ref.10

Mutagenesis

161

D → A: Compromises interaction with PCF11. No effect on growth. Ref.8 Ref.10

Secondary structure

445

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q08685 [UniParc].

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

FASTA

445

50,226

        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' referencesShow '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. Kleine K. Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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. 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.

PIR

S67147.

RefSeq

NP_014893.1. NM_001183669.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2NPI	X-ray	2.95	A/B	2-445	[»]

ProteinModelPortal

Q08685.

SMR

Q08685. Positions 18-445.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1487N.

IntAct

Q08685. 9 interactions.

MINT

MINT-394953.

STRING

4932.YOR250C.

Proteomic databases

PaxDb

Q08685.

PeptideAtlas

Q08685.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOR250C; YOR250C; YOR250C.

GeneID

854424.

KEGG

sce:YOR250C.

Organism-specific databases

CYGD

YOR250c.

SGD

S000005776. CLP1.

Phylogenomic databases

eggNOG

COG5623.

GeneTree

ENSGT00390000000344.

HOGENOM

HOG000231935.

K14399.

OMA

GFSVQAP.

OrthoDB

EOG4FFH9N.

Enzyme and pathway databases

BioCyc

YEAST:G3O-33742-MONOMER.

Gene expression databases

Genevestigator

Q08685.

GermOnline

YOR250C. Saccharomyces cerevisiae.

Family and domain databases

HAMAP

MF_03035. Clp1.

InterPro

IPR027417. P-loop_NTPase.
IPR010655. Pre-mRNA_cleavage_cplxII_Clp1.
[Graphical view]

Pfam

PF06807. Clp1. 1 hit.
[Graphical view]

SUPFAM

SSF52540. SSF52540. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q08685.

NextBio

976637.

Entry information

Entry name

CLP1_YEAST

Accession

Primary (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:	May 29, 2013
This is version 92 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome XV

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents