Reviewed, UniProtKB/Swiss-Prot Q66JK4 (CLP1_XENTR)

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:	TEgg012h01.1

Organism

Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

Taxonomic identifier

8364 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Mesobatrachia › Pipoidea › Pipidae › Xenopodinae › Xenopus › Silurana

Protein attributes

Sequence length	437 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.
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 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
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 437	437	Polyribonucleotide 5'-hydroxyl-kinase Clp1		PRO_0000375171
Regions
	Nucleotide binding	131 – 138	8	ATP Potential

Sequences

	Sequence		Length	Mass (Da)
	Q66JK4-1 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 14DCD7DB75439AAA	FASTA	437	47,973
	10 20 30 40 50 60 MSSEDLSAPG PSAPDSSFTG PSTKFELERE TELRLEVEGT DPVRVELVSG LAEVFGTELT 70 80 90 100 110 120 RNKKYTFPPG SRAAIFTWHG CTVQLWGSPD VAYVSRDTPM LLYLNTQVGL EQMRAQAERE 130 140 150 160 170 180 GERGPRVLVA GPSDVGKSTL CRLLLNYAVR RGRRPTLVEL DVGQGSVSVP GTVGALCVER 190 200 210 220 230 240 PADVEEGFSA QAPLVYHFGS TTPGTNIKLY NKLTSRLAHV FNLRCDSNRR ASVSGCLINT 250 260 270 280 290 300 CGWVKGSGYQ ALIHAASAFE VDVVLVLDQE RLYNDLLRDL PHFVRTLLLP KSGGASERSK 310 320 330 340 350 360 ECRRESRDQR VREYFYGPRG SLYPHAFEIK FSEVRVYKVG APSIPDSCLP LGMSQEDNQL 370 380 390 400 410 420 KLVPVTPGRD MAHHLLSVVP LDGGGAEEGI EERSVAGFIV ITGVDTERQT LTVLSPAPRP 430 LPKCVLLIMD IRFMDLK

References

[1]	Sanger Xenopus tropicalis EST/cDNA project Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Egg.
[2]	NIH - Xenopus Gene Collection (XGC) project Submitted (AUG-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Embryo.

Cross-references

Sequence databases
EMBLGenBankDDBJ	CR848531 mRNA. Translation: CAJ83686.1. BC080880 mRNA. Translation: AAH80880.1.
RefSeq	NP_001008002.1.
UniGene	Str.3967
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	Q66JK4.
Genome annotation databases
Ensembl	ENSXETT00000015427; ENSXETP00000015427; ENSXETG00000007088; Xenopus tropicalis. [Genome view]
GeneID	493364.
KEGG	xtr:493364.
Organism-specific databases
CTD	493364.
Xenbase	XB-FEAT-1008969. clp1.
Phylogenomic databases
HOGENOM	Q66JK4.
HOVERGEN	Q66JK4.
OMA	VVLLPKS.
Gene expression databases
Bgee	Q66JK4.
Family and domain databases
InterPro	IPR010655. Clp1. [Graphical view]
Pfam	PF06807. Clp1. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CLP1_XENTR

Accession

Primary (citable) accession number: Q66JK4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 26, 2009
Last sequence update:	October 11, 2004
Last modified:	November 3, 2009
This is version 31 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Xenopus annotation project