Reviewed, UniProtKB/Swiss-Prot Q5PQL4 (CLP1_RAT)

Names and origin

Protein names

Recommended name:
    Polyribonucleotide 5'-hydroxyl-kinase Clp1
    EC=2.7.1.78
Alternative name(s):
    Polynucleotide kinase Clp1
    Pre-mRNA cleavage complex II protein Clp1

Gene names

Name:	Clp1
ORF Names:	rCG_26812

Organism

Rattus norvegicus (Rat)

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	425 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at transcript level.

General annotation (Comments)

Function	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. Appears to have roles 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. 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.
Catalytic activity	ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA. ATP + 5'-dephospho-RNA = ADP + 5'-phospho-RNA.
Cofactor	Magnesium, manganese or nickel By similarity.
Subunit structure	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 By similarity.
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the Clp1 family.

Ontologies

Keywords
Biological process	mRNA processing tRNA processing
Cellular component	Nucleus
Ligand	ATP-binding Magnesium Manganese Nickel Nucleotide-binding
Molecular function	Kinase Transferase
Gene Ontology (GO)
Biological process	mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW siRNA loading onto RISC involved in RNA interference Inferred from sequence or structural similarity. Source: UniProtKB tRNA splicing, via endonucleolytic cleavage and ligation Inferred from sequence or structural similarity. Source: UniProtKB targeting of mRNA for destruction involved in RNA interference Inferred from sequence or structural similarity. Source: UniProtKB
Cellular component	tRNA-intron endonuclease complex Inferred from sequence or structural similarity. Source: UniProtKB
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity Inferred from electronic annotation. Source: EC ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity Inferred from sequence or structural similarity. Source: UniProtKB magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW nickel ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 425	425	Polyribonucleotide 5'-hydroxyl-kinase Clp1		PRO_0000375168
Regions
	Nucleotide binding	121 – 128	8	ATP Potential

Sequences

	Sequence		Length	Mass (Da)
	Q5PQL4-1 [UniParc]. Last modified January 4, 2005. Version 1. Checksum: C1AED7978B383097	FASTA	425	47,738
	10 20 30 40 50 60 MSEESNDDKK PTTKFELERE TELRFEVEAS QSVQLELLAG MAEIFGTELT RNKKFTFDAG 70 80 90 100 110 120 AKVAVFTWHG CSLQLSGRTE VAYVSKDTPM LLYLNTHTAL EQMRRQAEKE EERGPRVMVV 130 140 150 160 170 180 GPTDVGKSTV CRLLLNYAVR LGRRPTYVEL DVGQGSVSIP GTMGALYIER PADVEEGFSI 190 200 210 220 230 240 QAPLVYHFGS TTPGTNIKLY NKITSRLADV FNQRCEVNRR ASVSGCVINT CGWVKGYGYQ 250 260 270 280 290 300 ALVHAASAFE VDVVVVLDQE RLYNELKRDL PHFVRTVLLP KSGGVVERSK DFRRECRDER 310 320 330 340 350 360 IREYFYGFRG CFYPHAFNVK FSDVKIYKVG APTIPDSCLP LGMSQEDNQL KLVPVTPGRD 370 380 390 400 410 420 MVHHLLSVST AEGTEENLSE TSVAGFIVVT SVDVEHQVFT VLSPAPRPLP KNFLLIMDIR FMDLK

References

[1]	Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Brown Norway.
[2]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Testis.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	CH473949 Genomic DNA. Translation: EDL79312.1. BC087130 mRNA. Translation: AAH87130.1.
IPI	IPI00193975.
RefSeq	NP_001009599.1.
UniGene	Rn.144332
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	Q5PQL4.
Genome annotation databases
Ensembl	ENSRNOT00000009726; ENSRNOP00000009726; ENSRNOG00000007416; Rattus norvegicus. [Genome view]
GeneID	311166.
KEGG	rno:311166.
UCSC	NM_001009599. rat.
Organism-specific databases
CTD	311166.
RGD	1307679. Clp1.
Phylogenomic databases
HOVERGEN	Q5PQL4.
OMA	VVLLPKS.
Gene expression databases
ArrayExpress	Q5PQL4.
Genevestigator	Q5PQL4.
Family and domain databases
InterPro	IPR010655. Clp1. [Graphical view]
Pfam	PF06807. Clp1. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	663086.

Entry information

Entry name

CLP1_RAT

Accession

Primary (citable) accession number: Q5PQL4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 26, 2009
Last sequence update:	January 4, 2005
Last modified:	November 3, 2009
This is version 33 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)