CLP1_ARATH
ID CLP1_ARATH Reviewed; 444 AA.
AC Q9SR06;
DT 03-APR-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Protein CLP1 homolog {ECO:0000255|HAMAP-Rule:MF_03035};
DE AltName: Full=CLP-like protein 3;
DE AltName: Full=Protein CLP-SIMILAR PROTEIN 3;
GN Name=CLPS3; OrderedLocusNames=At3g04680; ORFNames=F7O18.15;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP INTERACTION WITH CPSF30; PCFS1; PCFS5 AND PCFS4, GENE FAMILY, AND
RP NOMENCLATURE.
RX PubMed=18479511; DOI=10.1186/1471-2164-9-220;
RA Hunt A.G., Xu R., Addepalli B., Rao S., Forbes K.P., Meeks L.R., Xing D.,
RA Mo M., Zhao H., Bandyopadhyay A., Dampanaboina L., Marion A.,
RA Von Lanken C., Li Q.Q.;
RT "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of
RT protein-protein interactions and gene expression profiling.";
RL BMC Genomics 9:220-220(2008).
RN [5]
RP INTERACTION WITH PCFS4, AND SUBCELLULAR LOCATION.
RX PubMed=18298670; DOI=10.1111/j.1365-313x.2008.03455.x;
RA Xing D., Zhao H., Xu R., Li Q.Q.;
RT "Arabidopsis PCFS4, a homologue of yeast polyadenylation factor Pcf11p,
RT regulates FCA alternative processing and promotes flowering time.";
RL Plant J. 54:899-910(2008).
RN [6]
RP FUNCTION, INTERACTION WITH CPSF100; CPSF160 AND FY, AND SUBCELLULAR
RP LOCATION.
RX PubMed=18971429; DOI=10.1104/pp.108.129817;
RA Xing D., Zhao H., Li Q.Q.;
RT "Arabidopsis CLP1-SIMILAR PROTEIN3, an ortholog of human polyadenylation
RT factor CLP1, functions in gametophyte, embryo, and postembryonic
RT development.";
RL Plant Physiol. 148:2059-2069(2008).
RN [7]
RP INTERACTION WITH PCFS4 AND SYM5.
RX PubMed=19748916; DOI=10.1104/pp.109.142729;
RA Zhao H., Xing D., Li Q.Q.;
RT "Unique features of plant cleavage and polyadenylation specificity factor
RT revealed by proteomic studies.";
RL Plant Physiol. 151:1546-1556(2009).
CC -!- FUNCTION: Required for endonucleolytic cleavage during polyadenylation-
CC dependent pre-mRNA 3'-end formation (By similarity). Functions in
CC gametophyte, embryo and postembryotic development (PubMed:18971429).
CC {ECO:0000255|HAMAP-Rule:MF_03035, ECO:0000269|PubMed:18298670,
CC ECO:0000269|PubMed:18971429}.
CC -!- SUBUNIT: Interacts with PCFS4 and SYM5. Forms a complex with cleavage
CC and polyadenylation specificity factor (CPSF) subunits CPSF30, CPSF100,
CC PCFS1, PCFS4, PCFS5, CPSF160 and FY. {ECO:0000269|PubMed:18298670,
CC ECO:0000269|PubMed:18479511, ECO:0000269|PubMed:18971429,
CC ECO:0000269|PubMed:19748916}.
CC -!- INTERACTION:
CC Q9SR06; Q0WPF2: PCFS4; NbExp=3; IntAct=EBI-1775627, EBI-1775648;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03035,
CC ECO:0000269|PubMed:18971429}.
CC -!- SIMILARITY: Belongs to the Clp1 family. Clp1 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_03035}.
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DR EMBL; AC011437; AAF04897.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74118.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74119.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM65538.1; -; Genomic_DNA.
DR EMBL; AY062866; AAL32944.1; -; mRNA.
DR EMBL; AY128751; AAM91151.1; -; mRNA.
DR RefSeq; NP_001319471.1; NM_001337539.1.
DR RefSeq; NP_001327497.1; NM_001337540.1.
DR RefSeq; NP_187119.1; NM_111340.3.
DR AlphaFoldDB; Q9SR06; -.
DR SMR; Q9SR06; -.
DR BioGRID; 4961; 9.
DR IntAct; Q9SR06; 4.
DR STRING; 3702.AT3G04680.1; -.
DR PaxDb; Q9SR06; -.
DR PRIDE; Q9SR06; -.
DR ProteomicsDB; 246753; -.
DR EnsemblPlants; AT3G04680.1; AT3G04680.1; AT3G04680.
DR EnsemblPlants; AT3G04680.2; AT3G04680.2; AT3G04680.
DR EnsemblPlants; AT3G04680.3; AT3G04680.3; AT3G04680.
DR GeneID; 819626; -.
DR Gramene; AT3G04680.1; AT3G04680.1; AT3G04680.
DR Gramene; AT3G04680.2; AT3G04680.2; AT3G04680.
DR Gramene; AT3G04680.3; AT3G04680.3; AT3G04680.
DR KEGG; ath:AT3G04680; -.
DR Araport; AT3G04680; -.
DR TAIR; locus:2084938; AT3G04680.
DR eggNOG; KOG2749; Eukaryota.
DR HOGENOM; CLU_018195_1_0_1; -.
DR InParanoid; Q9SR06; -.
DR OMA; VQYVNCH; -.
DR OrthoDB; 814241at2759; -.
DR PhylomeDB; Q9SR06; -.
DR PRO; PR:Q9SR06; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SR06; baseline and differential.
DR Genevisible; Q9SR06; AT.
DR GO; GO:0005849; C:mRNA cleavage factor complex; IPI:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0051731; F:polynucleotide 5'-hydroxyl-kinase activity; IBA:GO_Central.
DR GO; GO:0009908; P:flower development; IMP:TAIR.
DR GO; GO:0006378; P:mRNA polyadenylation; IBA:GO_Central.
DR GO; GO:0006397; P:mRNA processing; IMP:TAIR.
DR GO; GO:0048827; P:phyllome development; IMP:TAIR.
DR GO; GO:0006396; P:RNA processing; IBA:GO_Central.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IBA:GO_Central.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IMP:TAIR.
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; 1.
PE 1: Evidence at protein level;
KW ATP-binding; mRNA processing; Nucleotide-binding; Nucleus;
KW Reference proteome.
FT CHAIN 1..444
FT /note="Protein CLP1 homolog"
FT /id="PRO_0000421923"
FT BINDING 33
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 140..145
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035"
SQ SEQUENCE 444 AA; 48421 MW; 04968918D3A539AA CRC64;
MAYGGPSMNP PALSGAVPGS ANLKQVKLER ESELRIEVSE EPLRLRVVNG TAEIFGSELP
PEIWRTFPPR MKFAVFTWYG ATIEMDGVTE TDYTADETPM VSYINVHAIL DARRRFAKAS
TSNDPESSQG PRVIVVGPTD SGKSTLTKML LSWAAKQGWR PTFVDLDVGQ GSITIPGSIA
AAPIEMPLDP VEGFPLDMAL VYYYGHASPN MNVELYKALV KELAQVLEKQ FVGNPESRAA
GMVINTMGWI EGIGYELLLH AIDTFNASVV LVLGQEKLFS RLKDVLRSKS NVDVVKLHKS
GGVVARVKEV RKRSRNFKIQ EYFYGLSKEL SPYANTSSFS DLQVFRIGGG PQAPKSALPA
GSTSVSNPLR VTPVNIDDRD LLHSVLAVSY AEEPDQIISS NVSGFVYVTE VNVQKKKITY
LAPSPGTLPS KLLVAGSLAW LESV
