Q5PQL4 (CLP1_RAT) Reviewed, UniProtKB/Swiss-Prot
Last modified
May 1, 2013.
Version 58.
History...
Clusters with 
Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: Polyribonucleotide 5'-hydroxyl-kinase Clp1 EC=2.7.1.78 Alternative name(s): Polyadenylation factor Clp1 Polynucleotide kinase Clp1 Pre-mRNA cleavage complex II protein Clp1 | ||
| Gene names |
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| Organism | Rattus norvegicus (Rat) [Reference proteome] | ||
| 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. |
| 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. HAMAP-Rule MF_03035 |
| Catalytic activity | ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA. HAMAP-Rule MF_03035 ATP + 5'-dephospho-RNA = ADP + 5'-phospho-RNA. HAMAP-Rule MF_03035 |
| 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. Clp1 subfamily. |
Ontologies
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 425 | 425 | Polyribonucleotide 5'-hydroxyl-kinase Clp1 HAMAP-Rule MF_03035 | PRO_0000375168 | |||||
Regions | |||||||||
| Nucleotide binding | 124 – 129 | 6 | ATP By similarity | ||||||
Sites | |||||||||
| Binding site | 22 | 1 | ATP By similarity | ||||||
| Binding site | 62 | 1 | ATP; via carbonyl oxygen By similarity | ||||||
Sequences
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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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Testis. |
Cross-references
Sequence databases | |
|---|---|
| EMBL GenBank DDBJ | CH473949 Genomic DNA. Translation: EDL79312.1. BC087130 mRNA. Translation: AAH87130.1. |
| IPI | IPI00193975. |
| RefSeq | NP_001009599.1. NM_001009599.1. |
| UniGene | Rn.144332. |
3D structure databases | |
| ProteinModelPortal | Q5PQL4. |
| SMR | Q5PQL4. Positions 14-423. |
| ModBase | Search... |
Protein-protein interaction databases | |
| STRING | 10116.ENSRNOP00000009726. |
Proteomic databases | |
| PaxDb | Q5PQL4. |
Protocols and materials databases | |
| StructuralBiologyKnowledgebase | Search... |
Genome annotation databases | |
| Ensembl | ENSRNOT00000009726; ENSRNOP00000009726; ENSRNOG00000007416. |
| GeneID | 311166. |
| KEGG | rno:311166. |
| UCSC | RGD:1307679. rat. |
Organism-specific databases | |
| CTD | 10978. |
| RGD | 1307679. Clp1. |
Phylogenomic databases | |
| eggNOG | COG5623. |
| GeneTree | ENSGT00390000000344. |
| HOGENOM | HOG000231935. |
| InParanoid | Q5PQL4. |
| KO | K14399. |
| OMA | GFSVQAP. |
| OrthoDB | EOG4K0QNF. |
Gene expression databases | |
| Genevestigator | Q5PQL4. |
Family and domain databases | |
| HAMAP | MF_03035. Clp1. |
| InterPro | IPR010655. Pre-mRNA_cleavage_cplxII_Clp1. [Graphical view] |
| Pfam | PF06807. Clp1. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Other | |
| NextBio | 663086. |
Entry information
| Entry name | CLP1_RAT | ||||||||
| Accession | Primary (citable) accession number: Q5PQL4 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Chordata Protein Annotation Program | ||||||||
Relevant documents
| SIMILARITY comments Index of protein domains and families |