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Protein

Polyribonucleotide 5'-hydroxyl-kinase Clp1

Gene

Clp1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Polynucleotide kinase that can phosphorylate the 5'-hydroxyl groups of double-stranded RNA (dsRNA), single-stranded RNA (ssRNA), double-stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA is phosphorylated more efficiently than dsDNA, and the RNA component of a DNA:RNA hybrid is phosphorylated more efficiently than the DNA component. Plays a key role in both tRNA splicing and mRNA 3'-end formation. Component of the tRNA splicing endonuclease complex: phosphorylates the 5'-terminus of the tRNA 3'-exon during tRNA splicing; this phosphorylation event is a prerequisite for the subsequent ligation of the two exon halves and the production of a mature tRNA. Its role in tRNA splicing and maturation is required for cerebellar development. Component of the pre-mRNA cleavage complex II (CF-II), which seems to be required for mRNA 3'-end formation. Also phosphorylates the 5'-terminus of exogenously introduced short interfering RNAs (siRNAs), which is a necessary prerequisite for their incorporation into the RNA-induced silencing complex (RISC). However, endogenous siRNAs and microRNAs (miRNAs) that are produced by the cleavage of dsRNA precursors by DICER1 already contain a 5'-phosphate group, so this protein may be dispensible for normal RNA-mediated gene silencing (By similarity).By similarity

Catalytic activityi

ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.UniRule annotation
ATP + 5'-dephospho-RNA = ADP + 5'-phospho-RNA.UniRule annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation, Ni2+UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei22ATPUniRule annotation1
Binding sitei62ATP; via carbonyl oxygenUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi124 – 129ATPUniRule annotation6

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionKinase, Transferase
Biological processmRNA processing, tRNA processing
LigandATP-binding, Magnesium, Manganese, Nickel, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-RNO-109688 Cleavage of Growing Transcript in the Termination Region
R-RNO-72163 mRNA Splicing - Major Pathway
R-RNO-72187 mRNA 3'-end processing
R-RNO-77595 Processing of Intronless Pre-mRNAs

Names & Taxonomyi

Protein namesi
Recommended name:
Polyribonucleotide 5'-hydroxyl-kinase Clp1UniRule annotation (EC:2.7.1.78UniRule annotation)
Alternative name(s):
Polyadenylation factor Clp1UniRule annotation
Polynucleotide kinase Clp1UniRule annotation
Pre-mRNA cleavage complex II protein Clp1UniRule annotation
Gene namesi
Name:Clp1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 3

Organism-specific databases

RGDi1307679 Clp1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003751681 – 425Polyribonucleotide 5'-hydroxyl-kinase Clp1Add BLAST425

Proteomic databases

PaxDbiQ5PQL4

Expressioni

Gene expression databases

BgeeiENSRNOG00000007416
GenevisibleiQ5PQL4 RN

Interactioni

Subunit structurei

Component of the tRNA splicing endonuclease complex, composed of CLP1, TSEN2, TSEN15, TSEN34 and TSEN54. Component of pre-mRNA cleavage complex II (CF-II). Also associates with numerous components of the pre-mRNA cleavage complex I (CF-I/CFIm), including NUDT21, CPSF2, CPSF3, CPSF6 and CPSF7. Interacts with CSTF2 and SYMPK.UniRule annotation

Protein-protein interaction databases

BioGridi259846, 1 interactor
STRINGi10116.ENSRNOP00000009726

Structurei

3D structure databases

ProteinModelPortaliQ5PQL4
SMRiQ5PQL4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the Clp1 family. Clp1 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiKOG2749 Eukaryota
COG5623 LUCA
GeneTreeiENSGT00390000000344
HOGENOMiHOG000231935
InParanoidiQ5PQL4
KOiK14399
OMAiKVAIFTY
OrthoDBiEOG091G088L
PhylomeDBiQ5PQL4
TreeFamiTF105795

Family and domain databases

Gene3Di2.60.120.1030, 1 hit
3.30.70.2410, 1 hit
HAMAPiMF_03035 Clp1, 1 hit
InterProiView protein in InterPro
IPR028606 Clp1
IPR010655 Clp1_C
IPR038238 Clp1_C_sf
IPR032324 Clp1_N
IPR038239 Clp1_N_sf
IPR032319 CLP1_P
IPR027417 P-loop_NTPase
PfamiView protein in Pfam
PF06807 Clp1, 1 hit
PF16573 CLP1_N, 1 hit
PF16575 CLP1_P, 1 hit
SUPFAMiSSF52540 SSF52540, 2 hits

Sequencei

Sequence statusi: Complete.

Q5PQL4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEESNDDKK PTTKFELERE TELRFEVEAS QSVQLELLAG MAEIFGTELT
60 70 80 90 100
RNKKFTFDAG AKVAVFTWHG CSLQLSGRTE VAYVSKDTPM LLYLNTHTAL
110 120 130 140 150
EQMRRQAEKE EERGPRVMVV GPTDVGKSTV CRLLLNYAVR LGRRPTYVEL
160 170 180 190 200
DVGQGSVSIP GTMGALYIER PADVEEGFSI QAPLVYHFGS TTPGTNIKLY
210 220 230 240 250
NKITSRLADV FNQRCEVNRR ASVSGCVINT CGWVKGYGYQ ALVHAASAFE
260 270 280 290 300
VDVVVVLDQE RLYNELKRDL PHFVRTVLLP KSGGVVERSK DFRRECRDER
310 320 330 340 350
IREYFYGFRG CFYPHAFNVK FSDVKIYKVG APTIPDSCLP LGMSQEDNQL
360 370 380 390 400
KLVPVTPGRD MVHHLLSVST AEGTEENLSE TSVAGFIVVT SVDVEHQVFT
410 420
VLSPAPRPLP KNFLLIMDIR FMDLK
Length:425
Mass (Da):47,738
Last modified:January 4, 2005 - v1
Checksum:iC1AED7978B383097
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CH473949 Genomic DNA Translation: EDL79312.1
BC087130 mRNA Translation: AAH87130.1
RefSeqiNP_001009599.1, NM_001009599.1
XP_006234524.1, XM_006234462.2
XP_017447198.1, XM_017591709.1
UniGeneiRn.144332

Genome annotation databases

EnsembliENSRNOT00000009726; ENSRNOP00000009726; ENSRNOG00000007416
GeneIDi311166
KEGGirno:311166
UCSCiRGD:1307679 rat

Similar proteinsi

Entry informationi

Entry nameiCLP1_RAT
AccessioniPrimary (citable) accession number: Q5PQL4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 26, 2009
Last sequence update: January 4, 2005
Last modified: May 23, 2018
This is version 94 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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