Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei33 – 331ATPUniRule annotation1 Publication
Binding sitei72 – 721ATP; via carbonyl oxygenUniRule annotation1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi133 – 1386ATPUniRule annotation1 Publication

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)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 CLP1PRO_0000076211Add
BLAST

Proteomic databases

MaxQBiQ08685.

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. 36 interactions.
DIPiDIP-1487N.
IntActiQ08685. 9 interactions.
MINTiMINT-394953.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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 18-445.
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

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
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 18-445.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34640. 36 interactions.
DIPiDIP-1487N.
IntActiQ08685. 9 interactions.
MINTiMINT-394953.

Proteomic databases

MaxQBiQ08685.

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

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: September 7, 2016
This is version 122 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.