ID A0A091CR80_FUKDA Unreviewed; 425 AA.
AC A0A091CR80;
DT 26-NOV-2014, integrated into UniProtKB/TrEMBL.
DT 26-NOV-2014, sequence version 1.
DT 27-MAR-2024, entry version 48.
DE RecName: Full=Polyribonucleotide 5'-hydroxyl-kinase Clp1 {ECO:0000256|HAMAP-Rule:MF_03035};
DE EC=2.7.1.78 {ECO:0000256|HAMAP-Rule:MF_03035};
DE AltName: Full=Polyadenylation factor Clp1 {ECO:0000256|HAMAP-Rule:MF_03035};
DE AltName: Full=Polynucleotide kinase Clp1 {ECO:0000256|HAMAP-Rule:MF_03035};
DE AltName: Full=Pre-mRNA cleavage complex II protein Clp1 {ECO:0000256|HAMAP-Rule:MF_03035};
GN Name=CLP1 {ECO:0000256|HAMAP-Rule:MF_03035};
GN ORFNames=H920_16811 {ECO:0000313|EMBL:KFO21699.1};
OS Fukomys damarensis (Damaraland mole rat) (Cryptomys damarensis).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Hystricomorpha; Bathyergidae;
OC Fukomys.
OX NCBI_TaxID=885580 {ECO:0000313|EMBL:KFO21699.1, ECO:0000313|Proteomes:UP000028990};
RN [1] {ECO:0000313|EMBL:KFO21699.1, ECO:0000313|Proteomes:UP000028990}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC TISSUE=Liver {ECO:0000313|EMBL:KFO21699.1};
RA Gladyshev V.N., Fang X.;
RT "The Damaraland mole rat (Fukomys damarensis) genome and evolution of
RT African mole rats.";
RL Submitted (NOV-2013) 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. Appears to have roles 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. Component of the pre-mRNA cleavage complex II (CF-II),
CC 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. {ECO:0000256|HAMAP-Rule:MF_03035}.
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:0000256|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:0000256|HAMAP-
CC Rule:MF_03035};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_03035};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_03035};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_03035};
CC -!- SUBUNIT: Component of the tRNA splicing endonuclease complex, composed
CC of CLP1, TSEN2, TSEN15, TSEN34 and TSEN54. Component of pre-mRNA
CC cleavage complex II (CF-II). Also associates with numerous components
CC of the pre-mRNA cleavage complex I (CF-I/CFIm), including NUDT21,
CC CPSF2, CPSF3, CPSF6 and CPSF7. Interacts with CSTF2 and SYMPK.
CC {ECO:0000256|HAMAP-Rule:MF_03035}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123,
CC ECO:0000256|HAMAP-Rule:MF_03035}.
CC -!- SIMILARITY: Belongs to the Clp1 family. Clp1 subfamily.
CC {ECO:0000256|HAMAP-Rule:MF_03035}.
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DR EMBL; KN124308; KFO21699.1; -; Genomic_DNA.
DR RefSeq; XP_010606614.1; XM_010608312.1.
DR AlphaFoldDB; A0A091CR80; -.
DR STRING; 885580.ENSFDAP00000013549; -.
DR Ensembl; ENSFDAT00000026465; ENSFDAP00000013549; ENSFDAG00000000234.
DR GeneID; 104851138; -.
DR CTD; 10978; -.
DR eggNOG; KOG2749; Eukaryota.
DR OMA; VQYVNCH; -.
DR OrthoDB; 56092at2759; -.
DR Proteomes; UP000028990; Unassembled WGS sequence.
DR GO; GO:0005849; C:mRNA cleavage factor complex; IEA:UniProtKB-UniRule.
DR GO; GO:0000214; C:tRNA-intron endonuclease complex; IEA:UniProtKB-UniRule.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046404; F:ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0051736; F:ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0031124; P:mRNA 3'-end processing; IEA:UniProtKB-UniRule.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0070922; P:RISC complex assembly; IEA:UniProtKB-UniRule.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IEA:UniProtKB-UniRule.
DR CDD; cd01983; SIMIBI; 1.
DR Gene3D; 2.60.120.1030; Clp1, DNA binding domain; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR Gene3D; 2.40.30.330; Pre-mRNA cleavage complex subunit Clp1, C-terminal domain; 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; CLEAVAGE/POLYADENYLATION FACTOR IA SUBUNIT CLP1P; 1.
DR PANTHER; PTHR12755:SF6; POLYRIBONUCLEOTIDE 5'-HYDROXYL-KINASE CLP1; 1.
DR Pfam; PF06807; Clp1; 1.
DR Pfam; PF16573; CLP1_N; 1.
DR Pfam; PF16575; CLP1_P; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 2.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_03035};
KW Kinase {ECO:0000256|HAMAP-Rule:MF_03035, ECO:0000313|EMBL:KFO21699.1};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_03035};
KW Manganese {ECO:0000256|HAMAP-Rule:MF_03035};
KW mRNA processing {ECO:0000256|ARBA:ARBA00022664, ECO:0000256|HAMAP-
KW Rule:MF_03035};
KW Nickel {ECO:0000256|ARBA:ARBA00022596, ECO:0000256|HAMAP-Rule:MF_03035};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_03035};
KW Nucleus {ECO:0000256|ARBA:ARBA00023242, ECO:0000256|HAMAP-Rule:MF_03035};
KW Reference proteome {ECO:0000313|Proteomes:UP000028990};
KW Transferase {ECO:0000256|HAMAP-Rule:MF_03035};
KW tRNA processing {ECO:0000256|HAMAP-Rule:MF_03035}.
FT DOMAIN 16..107
FT /note="Clp1 N-terminal beta-sandwich"
FT /evidence="ECO:0000259|Pfam:PF16573"
FT DOMAIN 121..307
FT /note="Polyribonucleotide 5'-hydroxyl-kinase Clp1 P-loop"
FT /evidence="ECO:0000259|Pfam:PF16575"
FT DOMAIN 313..423
FT /note="Pre-mRNA cleavage complex subunit Clp1 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF06807"
FT BINDING 22
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03035"
FT BINDING 62
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03035"
FT BINDING 124..129
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03035"
SQ SEQUENCE 425 AA; 47615 MW; 9E5A025770E5C897 CRC64;
MGEEANDDKK PTTKFELERE TELRFEVEAS QSVQLELLAG MAEIFGTELT RNKKFTFDAG
AKVAVFTWHG CSVQLSGRTE VAYVSKDTPM LLYLNTHTAL EQMRRQAEKE EERGPRVMVV
GPTDVGKSTV CRLLLNYAVR LGRRPTYVEL DVGQGSVSIP GTMGALYIER PADVEEGFSI
QAPLVYHFGS TTPGTNIKLY NKITSRLADV FNQRCEVNRR ASVSGCVINT CGWVKGSGYQ
ALVHAASAFE VDVVVVLDQE RLYNELKRDL PHFVRTVLLP KSGGVVERSK DFRRECRDER
IREYFYGFRG CFYPHAFNVK FSDVKIYKVG APTIPDSCLP LGMSQEDNQL KLVPVTPGRD
MVHHLLSVST AEGTEENLSE TSVAGFIVVT SVDLEHQVFT VLSPAPRPLP KNFLLIMDIR
FMDLK
//
