Reviewed, UniProtKB/Swiss-Prot Q99LI9 (CLP1_MOUSE)

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

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	425 AA.
Sequence status	Complete.
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	Mo-molybdopterin cofactor biosynthetic process Inferred from electronic annotation. Source: InterPro 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 GTP binding Inferred from electronic annotation. Source: InterPro 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_0000089864
Regions
	Nucleotide binding	121 – 128	8	ATP Potential

Sequences

	Sequence		Length	Mass (Da)
	Q99LI9-1 [UniParc]. Last modified June 1, 2001. 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]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed: 16141072] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: C57BL/6J. Tissue: Embryo.
[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]. Strain: FVB/N. Tissue: Mammary tumor.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AK077647 mRNA. Translation: BAC36924.1. BC003237 mRNA. Translation: AAH03237.1.
IPI	IPI00116934.
RefSeq	NP_598601.1.
UniGene	Mm.21583
3D structure databases
SMR	Q99LI9. Positions 13-423.
ModBase	Search...
Protein-protein interaction databases
STRING	Q99LI9.
PTM databases
PhosphoSite	Q99LI9.
Proteomic databases
PRIDE	Q99LI9.
Genome annotation databases
Ensembl	ENSMUST00000028475; ENSMUSP00000028475; ENSMUSG00000027079; Mus musculus. [Genome view]
GeneID	98985.
KEGG	mmu:98985.
UCSC	uc008kja.1. mouse.
Organism-specific databases
CTD	98985.
MGI	MGI:2138968. Clp1.
Phylogenomic databases
HOGENOM	HBG316814.
HOVERGEN	Q99LI9.
InParanoid	Q99LI9.
OMA	NISETSV.
PhylomeDB	Q99LI9.
Gene expression databases
ArrayExpress	Q99LI9.
Bgee	Q99LI9.
Genevestigator	Q99LI9.
GermOnline	ENSMUSG00000027079. Mus musculus.
Family and domain databases
ProtoNet	Search...
Other Resources
NextBio	353735.
SOURCE	Search...

Entry information

Entry name

CLP1_MOUSE

Accession

Primary (citable) accession number: Q99LI9

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 4, 2005
Last sequence update:	June 1, 2001
Last modified:	February 9, 2010
This is version 52 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)