Reviewed, UniProtKB/Swiss-Prot Q6NS21 (CLP1_XENLA)

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

Xenopus laevis (African clawed frog)

Taxonomic identifier

8355 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	439 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 – 439	439	Polyribonucleotide 5'-hydroxyl-kinase Clp1		PRO_0000375170
Regions
	Nucleotide binding	133 – 140	8	ATP Potential

Sequences

	Sequence		Length	Mass (Da)
	Q6NS21-1 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: F76AC3E057E0072A	FASTA	439	48,336
	10 20 30 40 50 60 MSSEDLSAPG PSAPDSSWSS TGPSTKFELE RETELRLEVE GTDPVRVELV SGLAEVFGTE 70 80 90 100 110 120 LTRNKKYTFP PGSRAAIFTW HGCTVQLWGS PDMAYVSRDT PMLLYLNTQV GLEQMRVQAE 130 140 150 160 170 180 REGERGPRVL VAGPSDVGKS TLCRLLLNYA VRRGRRPTLV ELDVGQGSVS VPGTMGALCV 190 200 210 220 230 240 ERPADVEEGF SAQAPLVYHF GSTTPGTNIK LYNKLTSRLA HVFNLRCDSN RRASVSGCLI 250 260 270 280 290 300 NTCGWVKGSG YQALIHAASA FEVDVVLVLD QERLYNDLLR DLPHFVRTLL LPKSGGASER 310 320 330 340 350 360 SKECRRESRD QRVREYFYGP RGSLYPHAFE IKFSEVRVYK VGAPTIPDSC LPLGMSQEDN 370 380 390 400 410 420 QLKLVPVTPG RDMAHHLLSV VPLDGGSAEE GIEERSVAGF IVITGVDTER QTLTLLSPAP 430 RPLPKCVLLI MDIRFMDLK

References

[1]	NIH - Xenopus Gene Collection (XGC) project Submitted (MAY-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Embryo.

Cross-references

Sequence databases
EMBLGenBankDDBJ	BC070530 mRNA. Translation: AAH70530.1.
RefSeq	NP_001084787.1.
UniGene	Xl.30457
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	431824.
KEGG	xla:431824.
Organism-specific databases
CTD	431824.
Xenbase	XB-FEAT-1008969. clp1.
Phylogenomic databases
HOVERGEN	Q6NS21.
Family and domain databases
InterPro	IPR010655. Clp1. [Graphical view]
Pfam	PF06807. Clp1. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CLP1_XENLA

Accession

Primary (citable) accession number: Q6NS21

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 26, 2009
Last sequence update:	July 5, 2004
Last modified:	October 13, 2009
This is version 24 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Xenopus annotation project