CLO_ARATH
ID CLO_ARATH Reviewed; 987 AA.
AC Q9LNC5;
DT 06-JUL-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=110 kDa U5 small nuclear ribonucleoprotein component CLO {ECO:0000305};
DE AltName: Full=Protein CLOTHO {ECO:0000303|PubMed:18702672};
DE AltName: Full=Protein GAMETOPHYTE FACTOR 1 {ECO:0000303|Ref.4};
DE AltName: Full=Protein MATERNAL EFFECT EMBRYO ARREST 5 {ECO:0000305};
DE AltName: Full=Protein VAJRA-1 {ECO:0000303|PubMed:19168457};
DE AltName: Full=SNU114 homolog {ECO:0000305};
GN Name=CLO {ECO:0000303|PubMed:18702672};
GN Synonyms=GFA1 {ECO:0000303|Ref.4}, MEE5 {ECO:0000305},
GN VAJ-1 {ECO:0000303|PubMed:19168457};
GN OrderedLocusNames=At1g06220 {ECO:0000312|Araport:AT1G06220};
GN ORFNames=F9P14.8 {ECO:0000312|EMBL:AAF80219.1};
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX DOI=10.1007/s00497-007-0046-8;
RA Coury D.A., Zhang C., Ara Ko A., Skaggs M.I., Christensen C.A., Drews G.N.,
RA Feldmann K.A., Yadegari R.;
RT "Segregation distortion in Arabidopsis gametophytic factor 1 (gfa1) mutants
RT is caused by a deficiency of an essential RNA splicing factor.";
RL Sex. Plant Reprod. 20:87-97(2007).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=18702672; DOI=10.1111/j.1365-313x.2008.03650.x;
RA Moll C., von Lyncker L., Zimmermann S., Kaegi C., Baumann N., Twell D.,
RA Grossniklaus U., Gross-Hardt R.;
RT "CLO/GFA1 and ATO are novel regulators of gametic cell fate in plants.";
RL Plant J. 56:913-921(2008).
RN [6]
RP FUNCTION, INTERACTION WITH BRR2A AND PRP8A, AND DEVELOPMENTAL STAGE.
RX PubMed=19261069; DOI=10.1111/j.1744-7909.2008.00783.x;
RA Liu M., Yuan L., Liu N.Y., Shi D.Q., Liu J., Yang W.C.;
RT "GAMETOPHYTIC FACTOR 1, involved in pre-mRNA splicing, is essential for
RT megagametogenesis and embryogenesis in Arabidopsis.";
RL J. Integr. Plant Biol. 51:261-271(2009).
RN [7]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=19168457; DOI=10.1093/pcp/pcp011;
RA Yagi N., Takeda S., Matsumoto N., Okada K.;
RT "VAJ/GFA1/CLO is involved in the directional control of floral organ
RT growth.";
RL Plant Cell Physiol. 50:515-527(2009).
CC -!- FUNCTION: Splicing factor involved in pre-mRNA splicing and component
CC of the spliceosome (PubMed:18702672, PubMed:19168457). Essential for
CC reproduction. In female gametophyte, is necessary for the egg cell and
CC central cell fate determination and hence reproductive success.
CC Involved in a mechanism that prevents accessory cells from adopting
CC gametic cell fate. Is necessary to restrict LIS expression to interfere
CC with egg-cell specification (PubMed:18702672). Probable component of U5
CC small nuclear ribonucleoprotein (snRNP) that is required for pre-mRNA
CC splicing. Plays an essential role in female gametogenesis and embryo
CC development (PubMed:19261069). Required for the control of polarized
CC cell growth and cell proliferation during floral organ morphogenesis
CC (PubMed:19168457). {ECO:0000269|PubMed:18702672,
CC ECO:0000269|PubMed:19168457, ECO:0000269|PubMed:19261069}.
CC -!- SUBUNIT: Interacts with BRR2A and PRP8A. {ECO:0000269|PubMed:19261069}.
CC -!- SUBCELLULAR LOCATION: Nucleus speckle {ECO:0000269|PubMed:18702672,
CC ECO:0000269|PubMed:19168457}. Note=Colocalizes with CLO
CC (PubMed:18702672). Colocalizes with SC35 (PubMed:19168457).
CC {ECO:0000269|PubMed:18702672, ECO:0000269|PubMed:19168457}.
CC -!- TISSUE SPECIFICITY: Expressed in flower buds, open flowers and
CC siliques. Expressed at low levels in rosettes leaves, cauline leaves
CC and stems. {ECO:0000269|Ref.4}.
CC -!- DEVELOPMENTAL STAGE: Expressed in developing embryos until heart stage.
CC {ECO:0000269|PubMed:19261069}.
CC -!- DISRUPTION PHENOTYPE: Gametophytic lethality due to female gametophyte
CC defect, when homozygous. {ECO:0000269|PubMed:18702672,
CC ECO:0000269|Ref.4}.
CC -!- MISCELLANEOUS: This protein was named 'VAJRA', because the shape of
CC flower buds when ready to open resemble VAJRA, an instrument used in
CC esoteric Buddhism. {ECO:0000303|PubMed:19168457}.
CC -!- SIMILARITY: Belongs to the TRAFAC class translation factor GTPase
CC superfamily. Classic translation factor GTPase family.
CC {ECO:0000255|PROSITE-ProRule:PRU01059}.
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DR EMBL; AC025290; AAF80219.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27961.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27962.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58878.1; -; Genomic_DNA.
DR EMBL; AK226591; BAE98706.1; -; mRNA.
DR PIR; H86197; H86197.
DR RefSeq; NP_001321282.1; NM_001331621.1.
DR RefSeq; NP_172112.1; NM_100503.5.
DR RefSeq; NP_849600.1; NM_179269.4.
DR AlphaFoldDB; Q9LNC5; -.
DR SMR; Q9LNC5; -.
DR IntAct; Q9LNC5; 4.
DR STRING; 3702.AT1G06220.2; -.
DR iPTMnet; Q9LNC5; -.
DR PaxDb; Q9LNC5; -.
DR PRIDE; Q9LNC5; -.
DR ProteomicsDB; 246749; -.
DR EnsemblPlants; AT1G06220.1; AT1G06220.1; AT1G06220.
DR EnsemblPlants; AT1G06220.2; AT1G06220.2; AT1G06220.
DR EnsemblPlants; AT1G06220.3; AT1G06220.3; AT1G06220.
DR GeneID; 837131; -.
DR Gramene; AT1G06220.1; AT1G06220.1; AT1G06220.
DR Gramene; AT1G06220.2; AT1G06220.2; AT1G06220.
DR Gramene; AT1G06220.3; AT1G06220.3; AT1G06220.
DR KEGG; ath:AT1G06220; -.
DR Araport; AT1G06220; -.
DR TAIR; locus:2038555; AT1G06220.
DR eggNOG; KOG0468; Eukaryota.
DR HOGENOM; CLU_002794_11_2_1; -.
DR InParanoid; Q9LNC5; -.
DR OMA; GPDEMGP; -.
DR OrthoDB; 140796at2759; -.
DR PhylomeDB; Q9LNC5; -.
DR PRO; PR:Q9LNC5; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9LNC5; baseline and differential.
DR GO; GO:0005576; C:extracellular region; HDA:TAIR.
DR GO; GO:0016607; C:nuclear speck; IDA:TAIR.
DR GO; GO:0009505; C:plant-type cell wall; HDA:TAIR.
DR GO; GO:1990904; C:ribonucleoprotein complex; IBA:GO_Central.
DR GO; GO:0071007; C:U2-type catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0046540; C:U4/U6 x U5 tri-snRNP complex; IBA:GO_Central.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003924; F:GTPase activity; IEA:InterPro.
DR GO; GO:0030623; F:U5 snRNA binding; IBA:GO_Central.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0048437; P:floral organ development; IMP:UniProtKB.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR GO; GO:0045694; P:regulation of embryo sac egg cell differentiation; IMP:TAIR.
DR CDD; cd04098; eEF2_C_snRNP; 1.
DR CDD; cd04167; Snu114p; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR035647; EFG_III/V.
DR InterPro; IPR000640; EFG_V-like.
DR InterPro; IPR004161; EFTu-like_2.
DR InterPro; IPR031950; EFTUD2_N.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR005225; Small_GTP-bd_dom.
DR InterPro; IPR044121; Snu114_GTP-bd.
DR InterPro; IPR000795; T_Tr_GTP-bd_dom.
DR InterPro; IPR009000; Transl_B-barrel_sf.
DR InterPro; IPR005517; Transl_elong_EFG/EF2_IV.
DR InterPro; IPR035655; U5-116kDa_C.
DR Pfam; PF00679; EFG_C; 1.
DR Pfam; PF03764; EFG_IV; 1.
DR Pfam; PF16004; EFTUD2; 1.
DR Pfam; PF00009; GTP_EFTU; 1.
DR Pfam; PF03144; GTP_EFTU_D2; 1.
DR PRINTS; PR00315; ELONGATNFCT.
DR SMART; SM00838; EFG_C; 1.
DR SMART; SM00889; EFG_IV; 1.
DR SUPFAM; SSF50447; SSF50447; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF54980; SSF54980; 2.
DR TIGRFAMs; TIGR00231; small_GTP; 1.
DR PROSITE; PS51722; G_TR_2; 1.
PE 1: Evidence at protein level;
KW GTP-binding; mRNA processing; mRNA splicing; Nucleotide-binding; Nucleus;
KW Reference proteome; Spliceosome.
FT CHAIN 1..987
FT /note="110 kDa U5 small nuclear ribonucleoprotein component
FT CLO"
FT /id="PRO_0000436561"
FT DOMAIN 136..422
FT /note="tr-type G"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01059"
FT REGION 1..54
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 145..152
FT /note="G1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01059"
FT REGION 189..193
FT /note="G2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01059"
FT REGION 215..218
FT /note="G3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01059"
FT REGION 269..272
FT /note="G4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01059"
FT REGION 395..397
FT /note="G5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01059"
FT COMPBIAS 19..33
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 145..152
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255"
FT BINDING 215..219
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255"
FT BINDING 269..272
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255"
SQ SEQUENCE 987 AA; 110442 MW; 868DD5F6597FBB79 CRC64;
MESSLYDEFG NYVGPEIESD RDSDDEVEDE DLQDKHLEEN GSDGEQGPGG SNGWITTIND
VEMENQIVLP EDKKYYPTAE EVYGEDVETL VMDEDEQPLE QPIIKPVRDI RFEVGVKDQA
TYVSTQFLIG LMSNPALVRN VALVGHLQHG KTVFMDMLVE QTHHMSTFNA KNEKHMKYTD
TRVDEQERNI SIKAVPMSLV LEDSRSKSYL CNIMDTPGHV NFSDEMTASL RLADGAVLIV
DAAEGVMVNT ERAIRHAIQD HLPIVVVINK VDRLITELKL PPRDAYYKLR HTIEVINNHI
SAASTTAGDL PLIDPAAGNV CFASGTAGWS FTLQSFAKMY AKLHGVAMDV DKFASRLWGD
VYYHSDTRVF KRSPPVGGGE RAFVQFILEP LYKIYSQVIG EHKKSVETTL AELGVTLSNS
AYKLNVRPLL RLACSSVFGS ASGFTDMLVK HIPSPREAAA RKVDHSYTGT KDSPIYESMV
ECDPSGPLMV NVTKLYPKSD TSVFDVFGRV YSGRLQTGQS VRVLGEGYSP EDEEDMTIKE
VTKLWIYQAR YRIPVSSAPP GSWVLIEGVD ASIMKTATLC NASYDEDVYI FRALQFNTLP
VVKTATEPLN PSELPKMVEG LRKISKSYPL AITKVEESGE HTILGTGELY LDSIMKDLRE
LYSEVEVKVA DPVVSFCETV VESSSMKCFA ETPNKKNKIT MIAEPLDRGL AEDIENGVVS
IDWNRKQLGD FFRTKYDWDL LAARSIWAFG PDKQGPNILL DDTLPTEVDR NLMMAVKDSI
VQGFQWGARE GPLCDEPIRN VKFKIVDARI APEPLHRGSG QMIPTARRVA YSAFLMATPR
LMEPVYYVEI QTPIDCVTAI YTVLSRRRGH VTSDVPQPGT PAYIVKAFLP VIESFGFETD
LRYHTQGQAF CLSVFDHWAI VPGDPLDKAI QLRPLEPAPI QHLAREFMVK TRRRKGMSED
VSGNKFFDEA MMVELAQQTG DLHLQMI
