CLP1_XENTR
ID CLP1_XENTR Reviewed; 437 AA.
AC Q66JK4;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Polyribonucleotide 5'-hydroxyl-kinase Clp1 {ECO:0000255|HAMAP-Rule:MF_03035};
DE EC=2.7.1.78 {ECO:0000255|HAMAP-Rule:MF_03035};
DE AltName: Full=Polyadenylation factor Clp1 {ECO:0000255|HAMAP-Rule:MF_03035};
DE AltName: Full=Polynucleotide kinase Clp1 {ECO:0000255|HAMAP-Rule:MF_03035};
DE AltName: Full=Pre-mRNA cleavage complex II protein Clp1 {ECO:0000255|HAMAP-Rule:MF_03035};
GN Name=clp1; ORFNames=TEgg012h01.1;
OS Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana.
OX NCBI_TaxID=8364;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Egg;
RG Sanger Xenopus tropicalis EST/cDNA project;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (AUG-2004) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Polynucleotide kinase that can phosphorylate the 5'-hydroxyl
CC groups of double-stranded RNA (dsRNA), single-stranded RNA (ssRNA),
CC double stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA
CC is phosphorylated more efficiently than dsDNA, and the RNA component of
CC a DNA:RNA hybrid is phosphorylated more efficiently than the DNA
CC component. Plays a role in both tRNA splicing and mRNA 3'-end
CC formation. Component of the tRNA splicing endonuclease complex:
CC phosphorylates the 5'-terminus of the tRNA 3'-exon during tRNA
CC splicing; this phosphorylation event is a prerequisite for the
CC subsequent ligation of the two exon halves and the production of a
CC mature tRNA. Its role in tRNA splicing and maturation is required for
CC cerebellar development. Component of the pre-mRNA cleavage complex II
CC (CF-II), which seems to be required for mRNA 3'-end formation. Also
CC phosphorylates the 5'-terminus of exogenously introduced short
CC interfering RNAs (siRNAs), which is a necessary prerequisite for their
CC incorporation into the RNA-induced silencing complex (RISC). However,
CC endogenous siRNAs and microRNAs (miRNAs) that are produced by the
CC cleavage of dsRNA precursors by dicer1 already contain a 5'-phosphate
CC group, so this protein may be dispensible for normal RNA-mediated gene
CC silencing (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP = a 5'-end
CC 5'-monophospho-2'-deoxyribonucleoside-DNA + ADP + H(+);
CC Xref=Rhea:RHEA:15669, Rhea:RHEA-COMP:13180, Rhea:RHEA-COMP:13184,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:136412,
CC ChEBI:CHEBI:136416, ChEBI:CHEBI:456216; EC=2.7.1.78;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03035};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end dephospho-ribonucleoside-RNA + ATP = a 5'-end 5'-
CC monophospho-ribonucleoside-RNA + ADP + H(+); Xref=Rhea:RHEA:54580,
CC Rhea:RHEA-COMP:13935, Rhea:RHEA-COMP:13936, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:138282, ChEBI:CHEBI:138284,
CC ChEBI:CHEBI:456216; EC=2.7.1.78; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03035};
CC -!- SUBUNIT: Component of the tRNA splicing endonuclease complex. Component
CC of pre-mRNA cleavage complex II (CF-II). {ECO:0000255|HAMAP-
CC Rule:MF_03035}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03035}.
CC -!- SIMILARITY: Belongs to the Clp1 family. Clp1 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_03035}.
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DR EMBL; CR848531; CAJ83686.1; -; mRNA.
DR EMBL; BC080880; AAH80880.1; -; mRNA.
DR RefSeq; NP_001008002.1; NM_001008001.1.
DR RefSeq; XP_017950844.1; XM_018095355.1.
DR AlphaFoldDB; Q66JK4; -.
DR SMR; Q66JK4; -.
DR STRING; 8364.ENSXETP00000009421; -.
DR PaxDb; Q66JK4; -.
DR DNASU; 493364; -.
DR GeneID; 493364; -.
DR KEGG; xtr:493364; -.
DR CTD; 10978; -.
DR Xenbase; XB-GENE-1008970; clp1.
DR eggNOG; KOG2749; Eukaryota.
DR HOGENOM; CLU_018195_1_0_1; -.
DR InParanoid; Q66JK4; -.
DR OMA; GENQWER; -.
DR OrthoDB; 814241at2759; -.
DR PhylomeDB; Q66JK4; -.
DR TreeFam; TF105795; -.
DR Reactome; R-XTR-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-XTR-72187; mRNA 3'-end processing.
DR Proteomes; UP000008143; Chromosome 7.
DR Proteomes; UP000790000; Unplaced.
DR Bgee; ENSXETG00000007088; Expressed in early embryo and 14 other tissues.
DR ExpressionAtlas; Q66JK4; baseline.
DR GO; GO:0005849; C:mRNA cleavage factor complex; IEA:UniProtKB-UniRule.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000214; C:tRNA-intron endonuclease complex; ISS:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046404; F:polydeoxyribonucleotide 5'-hydroxyl-kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0051733; F:polydeoxyribonucleotide kinase activity; ISS:UniProtKB.
DR GO; GO:0051731; F:polynucleotide 5'-hydroxyl-kinase activity; IBA:GO_Central.
DR GO; GO:0051736; F:polyribonucleotide 5'-hydroxyl-kinase activity; ISS:UniProtKB.
DR GO; GO:0021695; P:cerebellar cortex development; ISS:UniProtKB.
DR GO; GO:0098795; P:global gene silencing by mRNA cleavage; ISS:UniProtKB.
DR GO; GO:0006378; P:mRNA polyadenylation; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0070922; P:RISC complex assembly; ISS:UniProtKB.
DR GO; GO:0006396; P:RNA processing; IBA:GO_Central.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; ISS:UniProtKB.
DR Gene3D; 2.40.30.330; -; 1.
DR Gene3D; 2.60.120.1030; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_03035; Clp1; 1.
DR InterPro; IPR028606; Clp1.
DR InterPro; IPR045116; Clp1/Grc3.
DR InterPro; IPR010655; Clp1_C.
DR InterPro; IPR038238; Clp1_C_sf.
DR InterPro; IPR032324; Clp1_N.
DR InterPro; IPR038239; Clp1_N_sf.
DR InterPro; IPR032319; CLP1_P.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR12755; PTHR12755; 1.
DR Pfam; PF06807; Clp1; 1.
DR Pfam; PF16573; CLP1_N; 1.
DR Pfam; PF16575; CLP1_P; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
PE 2: Evidence at transcript level;
KW ATP-binding; Kinase; mRNA processing; Nucleotide-binding; Nucleus;
KW Reference proteome; Transferase; tRNA processing.
FT CHAIN 1..437
FT /note="Polyribonucleotide 5'-hydroxyl-kinase Clp1"
FT /id="PRO_0000375171"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..24
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 32
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035"
FT BINDING 72
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035"
FT BINDING 134..139
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035"
SQ SEQUENCE 437 AA; 47973 MW; 14DCD7DB75439AAA CRC64;
MSSEDLSAPG PSAPDSSFTG PSTKFELERE TELRLEVEGT DPVRVELVSG LAEVFGTELT
RNKKYTFPPG SRAAIFTWHG CTVQLWGSPD VAYVSRDTPM LLYLNTQVGL EQMRAQAERE
GERGPRVLVA GPSDVGKSTL CRLLLNYAVR RGRRPTLVEL DVGQGSVSVP GTVGALCVER
PADVEEGFSA QAPLVYHFGS TTPGTNIKLY NKLTSRLAHV FNLRCDSNRR ASVSGCLINT
CGWVKGSGYQ ALIHAASAFE VDVVLVLDQE RLYNDLLRDL PHFVRTLLLP KSGGASERSK
ECRRESRDQR VREYFYGPRG SLYPHAFEIK FSEVRVYKVG APSIPDSCLP LGMSQEDNQL
KLVPVTPGRD MAHHLLSVVP LDGGGAEEGI EERSVAGFIV ITGVDTERQT LTVLSPAPRP
LPKCVLLIMD IRFMDLK
