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Protein

mRNA cleavage and polyadenylation factor CLP1

Gene

CLP1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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.UniRule annotation4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei33ATPUniRule annotation1 Publication1
Binding sitei72ATP; via carbonyl oxygenUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi133 – 138ATPUniRule annotation1 Publication6

GO - Molecular functioni

GO - Biological processi

  • gene looping Source: SGD
  • mRNA 3'-end processing Source: SGD
  • mRNA polyadenylation Source: SGD
  • pre-mRNA cleavage required for polyadenylation Source: SGD
  • tRNA splicing, via endonucleolytic cleavage and ligation Source: GO_Central
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 CLP1UniRule annotation
Gene namesi
Name:CLP1UniRule annotation
Ordered Locus Names:YOR250C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR250C.
SGDiS000005776. CLP1.

Subcellular locationi

  • Nucleus UniRule annotation

GO - Cellular componenti

  • 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)DescriptionActionsGraphical viewLength
Mutagenesisi136K → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-137. 1 Publication1
Mutagenesisi137T → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-136. 1 Publication1
Mutagenesisi161D → A: Compromises interaction with PCF11. No effect on growth. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000762111 – 445mRNA cleavage and polyadenylation factor CLP1Add BLAST445

Proteomic databases

MaxQBiQ08685.
PRIDEiQ08685.

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 SSU72.5 Publications

Binary interactionsi

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

Protein-protein interaction databases

BioGridi34640. 37 interactors.
DIPiDIP-1487N.
IntActiQ08685. 9 interactors.
MINTiMINT-394953.

Structurei

Secondary structure

1445
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi24 – 28Combined sources5
Beta strandi32 – 37Combined sources6
Beta strandi43 – 51Combined sources9
Beta strandi53 – 55Combined sources3
Beta strandi65 – 70Combined sources6
Beta strandi72 – 79Combined sources8
Beta strandi81 – 86Combined sources6
Turni92 – 94Combined sources3
Beta strandi96 – 99Combined sources4
Helixi103 – 119Combined sources17
Beta strandi120 – 122Combined sources3
Beta strandi125 – 131Combined sources7
Helixi136 – 147Combined sources12
Helixi148 – 151Combined sources4
Beta strandi156 – 159Combined sources4
Beta strandi166 – 168Combined sources3
Beta strandi172 – 177Combined sources6
Beta strandi194 – 196Combined sources3
Beta strandi206 – 209Combined sources4
Beta strandi212 – 214Combined sources3
Helixi215 – 217Combined sources3
Helixi219 – 239Combined sources21
Helixi241 – 246Combined sources6
Beta strandi248 – 251Combined sources4
Helixi255 – 257Combined sources3
Helixi263 – 271Combined sources9
Beta strandi276 – 281Combined sources6
Helixi286 – 299Combined sources14
Helixi301 – 303Combined sources3
Beta strandi304 – 307Combined sources4
Helixi318 – 334Combined sources17
Turni337 – 339Combined sources3
Beta strandi344 – 349Combined sources6
Helixi350 – 352Combined sources3
Beta strandi355 – 358Combined sources4
Helixi361 – 364Combined sources4
Beta strandi371 – 373Combined sources3
Helixi378 – 381Combined sources4
Beta strandi384 – 392Combined sources9
Helixi397 – 402Combined sources6
Beta strandi405 – 415Combined sources11
Turni416 – 419Combined sources4
Beta strandi420 – 430Combined sources11
Beta strandi434 – 442Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08685.

Family & Domainsi

Sequence similaritiesi

Belongs to the Clp1 family. Clp1 subfamily.UniRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000000344.
HOGENOMiHOG000231935.
InParanoidiQ08685.
KOiK14399.
OMAiHIVTEFA.
OrthoDBiEOG092C2S2R.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_03035. Clp1. 1 hit.
InterProiIPR028606. Clp1.
IPR032324. Clp1_N.
IPR032319. CLP1_P.
IPR027417. P-loop_NTPase.
IPR010655. Pre-mRNA_cleavage_Clp1.
[Graphical view]
PfamiPF06807. Clp1. 1 hit.
PF16573. CLP1_N. 1 hit.
PF16575. CLP1_P. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.

Sequencei

Sequence statusi: Complete.

Q08685-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASLPGIDEH TTSEELITGD NEWHKLVIPK GSDWQIDLKA EGKLIVKVNS
60 70 80 90 100
GIVEIFGTEL AVDDEYTFQN WKFPIYAVEE TELLWKCPDL TTNTITVKPN
110 120 130 140 150
HTMKYIYNLH FMLEKIRMSN FEGPRVVIVG GSQTGKTSLS RTLCSYALKF
160 170 180 190 200
NAYQPLYINL DPQQPIFTVP GCISATPISD ILDAQLPTWG QSLTSGATLL
210 220 230 240 250
HNKQPMVKNF GLERINENKD LYLECISQLG QVVGQRLHLD PQVRRSGCIV
260 270 280 290 300
DTPSISQLDE NLAELHHIIE KLNVNIMLVL CSETDPLWEK VKKTFGPELG
310 320 330 340 350
NNNIFFIPKL DGVSAVDDVY KRSLQRTSIR EYFYGSLDTA LSPYAIGVDY
360 370 380 390 400
EDLTIWKPSN VFDNEVGRVE LFPVTITPSN LQHAIIAITF AERRADQATV
410 420 430 440
IKSPILGFAL ITEVNEKRRK LRVLLPVPGR LPSKAMILTS YRYLE
Length:445
Mass (Da):50,226
Last modified:November 1, 1996 - v1
Checksum:iB00F7659E83090DA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34640. 37 interactors.
DIPiDIP-1487N.
IntActiQ08685. 9 interactors.
MINTiMINT-394953.

Proteomic databases

MaxQBiQ08685.
PRIDEiQ08685.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YOR250C.
SGDiS000005776. CLP1.

Phylogenomic databases

GeneTreeiENSGT00390000000344.
HOGENOMiHOG000231935.
InParanoidiQ08685.
KOiK14399.
OMAiHIVTEFA.
OrthoDBiEOG092C2S2R.

Enzyme and pathway databases

BioCyciYEAST:G3O-33742-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ08685.
PROiQ08685.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_03035. Clp1. 1 hit.
InterProiIPR028606. Clp1.
IPR032324. Clp1_N.
IPR032319. CLP1_P.
IPR027417. P-loop_NTPase.
IPR010655. Pre-mRNA_cleavage_Clp1.
[Graphical view]
PfamiPF06807. Clp1. 1 hit.
PF16573. CLP1_N. 1 hit.
PF16575. CLP1_P. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
ProtoNetiSearch...

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: November 30, 2016
This is version 125 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.Curated

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.