LCBK1_ARATH
ID LCBK1_ARATH Reviewed; 763 AA.
AC Q9LRB0; B9DHC8; Q9FHL3;
DT 04-DEC-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Sphingoid long-chain bases kinase 1;
DE Short=AtLCBK1;
DE Short=LCB kinase 1;
DE EC=2.7.-.-;
DE AltName: Full=Sphingosine kinase 1;
GN Name=LCBK1; OrderedLocusNames=At5g23450; ORFNames=K19M13.8;
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 [MRNA], FUNCTION, TISSUE SPECIFICITY, AND INDUCTION.
RC STRAIN=cv. Columbia;
RX PubMed=15695468; DOI=10.1093/pcp/pci023;
RA Imai H., Nishiura H.;
RT "Phosphorylation of sphingoid long-chain bases in Arabidopsis: functional
RT characterization and expression of the first sphingoid long-chain base
RT Kinase gene in plants.";
RL Plant Cell Physiol. 46:375-380(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10470850; DOI=10.1093/dnares/6.3.183;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Kotani H.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence
RT features of the regions of 1,011,550 bp covered by seventeen P1 and TAC
RT clones.";
RL DNA Res. 6:183-195(1999).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP IDENTIFICATION.
RX PubMed=11171192; DOI=10.1042/bst0280747;
RA Nishiura H., Tamura K., Morimoto Y., Imai H.;
RT "Characterization of sphingolipid long-chain base kinase in Arabidopsis
RT thaliana.";
RL Biochem. Soc. Trans. 28:747-748(2000).
RN [7]
RP CHARACTERIZATION.
RX PubMed=15665242; DOI=10.1104/pp.104.055806;
RA Coursol S., Le Stunff H., Lynch D.V., Gilroy S., Assmann S.M., Spiegel S.;
RT "Arabidopsis sphingosine kinase and the effects of phytosphingosine-1-
RT phosphate on stomatal aperture.";
RL Plant Physiol. 137:724-737(2005).
CC -!- FUNCTION: Involved in the production of sphingolipid metabolites.
CC Active on sphingosine, phytosphingosine (PHS, 4-hydroxysphinganine), D-
CC erythro-dihydrosphingosine, D-erythro-sphingosine and trans-4, trans-8-
CC sphingadienine, an LCB found exclusively in plants, but not on N-
CC acetyl-dihydrosphingosine (C2-dihydroceramide) and D-threo-
CC dihydrosphingosine. {ECO:0000269|PubMed:15695468}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9LRB0-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in roots, stems, leaves and at higher
CC levels in flowers. {ECO:0000269|PubMed:15695468}.
CC -!- INDUCTION: Not induced by low-humidity stress or by abscisic acid
CC treatment. {ECO:0000269|PubMed:15695468}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB09561.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB046717; BAB07787.1; -; mRNA.
DR EMBL; AB018110; BAB09561.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED93169.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93170.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM69595.1; -; Genomic_DNA.
DR EMBL; AY139759; AAM98080.1; -; mRNA.
DR EMBL; BT004544; AAO42790.1; -; mRNA.
DR EMBL; AK317480; BAH20145.1; -; mRNA.
DR RefSeq; NP_001331261.1; NM_001343804.1. [Q9LRB0-1]
DR RefSeq; NP_568432.1; NM_122252.4. [Q9LRB0-1]
DR RefSeq; NP_851065.1; NM_180734.3. [Q9LRB0-1]
DR AlphaFoldDB; Q9LRB0; -.
DR SMR; Q9LRB0; -.
DR BioGRID; 17686; 3.
DR IntAct; Q9LRB0; 2.
DR STRING; 3702.AT5G23450.3; -.
DR iPTMnet; Q9LRB0; -.
DR SwissPalm; Q9LRB0; -.
DR PaxDb; Q9LRB0; -.
DR PRIDE; Q9LRB0; -.
DR ProteomicsDB; 238556; -. [Q9LRB0-1]
DR EnsemblPlants; AT5G23450.1; AT5G23450.1; AT5G23450. [Q9LRB0-1]
DR EnsemblPlants; AT5G23450.2; AT5G23450.2; AT5G23450. [Q9LRB0-1]
DR EnsemblPlants; AT5G23450.5; AT5G23450.5; AT5G23450. [Q9LRB0-1]
DR GeneID; 832411; -.
DR Gramene; AT5G23450.1; AT5G23450.1; AT5G23450. [Q9LRB0-1]
DR Gramene; AT5G23450.2; AT5G23450.2; AT5G23450. [Q9LRB0-1]
DR Gramene; AT5G23450.5; AT5G23450.5; AT5G23450. [Q9LRB0-1]
DR KEGG; ath:AT5G23450; -.
DR Araport; AT5G23450; -.
DR eggNOG; KOG1116; Eukaryota.
DR InParanoid; Q9LRB0; -.
DR PhylomeDB; Q9LRB0; -.
DR BioCyc; ARA:AT5G23450-MON; -.
DR PRO; PR:Q9LRB0; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LRB0; baseline and differential.
DR Genevisible; Q9LRB0; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; IBA:GO_Central.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0017050; F:D-erythro-sphingosine kinase activity; IDA:UniProtKB.
DR GO; GO:0001727; F:lipid kinase activity; IBA:GO_Central.
DR GO; GO:0003951; F:NAD+ kinase activity; IEA:InterPro.
DR GO; GO:0016310; P:phosphorylation; IBA:GO_Central.
DR GO; GO:0030148; P:sphingolipid biosynthetic process; IDA:UniProtKB.
DR GO; GO:0006665; P:sphingolipid metabolic process; IBA:GO_Central.
DR GO; GO:0046512; P:sphingosine biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.40.50.10330; -; 1.
DR InterPro; IPR017438; ATP-NAD_kinase_N.
DR InterPro; IPR001206; Diacylglycerol_kinase_cat_dom.
DR InterPro; IPR016064; NAD/diacylglycerol_kinase_sf.
DR InterPro; IPR045540; YegS/DAGK_C.
DR Pfam; PF00781; DAGK_cat; 1.
DR Pfam; PF19279; YegS_C; 1.
DR SMART; SM00046; DAGKc; 1.
DR SUPFAM; SSF111331; SSF111331; 1.
DR PROSITE; PS50146; DAGK; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Kinase; Nucleotide-binding;
KW Reference proteome; Transferase.
FT CHAIN 1..763
FT /note="Sphingoid long-chain bases kinase 1"
FT /id="PRO_0000312001"
FT DOMAIN 245..384
FT /note="DAGKc"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT REGION 34..81
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 561..603
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 47..81
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 567..588
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 315
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 255..257
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 287
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 313..316
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 320
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 345..347
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 418
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 733..735
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT CONFLICT 22
FT /note="S -> P (in Ref. 5; BAH20145)"
FT /evidence="ECO:0000305"
FT CONFLICT 401
FT /note="S -> G (in Ref. 5; BAH20145)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 763 AA; 83592 MW; 870927E419B4277C CRC64;
MQKSGVNRNP SLKVAIPQAQ QSLRRLGFCS QIATGGSQQS SPIVFPEKRN KKVKASSRRG
EVTNDPQVKP KPDEHRIDIG GGDEKSDLLG SLVYAGKLVL DKRKSASGKD ATEIQQPAAT
DISIKKAVDA KLTSSALVWG SDMLQLNDVV SVTYNVGLRH FTVHAYPIGK GSCGLSCFTK
PKRSRKDFRF VAPTVEEAVQ WVASFGDQQC FINCLPHPLV AKKQASSELF SVPIDTPPEL
VFRCKSAPKM LVILNPRSGH GRSIKVFHNV VEPIFKLAGI KMEVVKTTKA GHARELASTV
DINLCSDGII CVGGDGIINE VLNGLLTRSN PKEGVSIPIG IVPAGSDNSL VWTVLGVRDP
ISAALSIVKG GLTATDVFAV EWIHTGIIHF GMTVSYYGFV SDVLELSEKY QKRFGPLRYF
VAGFLKFMCL PKYSYEVEYL PAQKEDAEGK IRLEKEAVDM QDLYTDVMRR SSREGFPRAS
SLSSIDSIMT PSVGELDTCS STHASTEPSE YVRGIDPKMK RLSSGRRDVT AEPEVIHPQA
QSTTPNWPRT RSKSRMDKGW MGLTSVQDPP TRCSWGNTGG QDREDISSTV SDPGPIWDAG
PKWDTEPSAW DVENSIELPG PPEDIETGLR KQSITPIFED KWVSRKGHFL GIMVCNHACR
TVQSSQVVAP NSEHDDGTMD MLLVHGCGRL RLLRFFILLQ TGRHLSLPYV ECVKVKSVKI
KAGKNTHDSC GIDGELFALH GEVISTMLPE QCRLIGNAPG RHS
