SPHK1_ARATH
ID SPHK1_ARATH Reviewed; 485 AA.
AC Q8L7L1; A0A2H1ZEN6; F4JJK0; O65419;
DT 01-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Sphingosine kinase 1;
DE EC=2.7.1.91 {ECO:0000269|PubMed:21330371};
GN Name=SPHK1; OrderedLocusNames=At4g21540; ORFNames=F18E5.160;
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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] (ISOFORM 1).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=18557834; DOI=10.1111/j.1365-313x.2008.03579.x;
RA Worrall D., Liang Y.K., Alvarez S., Holroyd G.H., Spiegel S.,
RA Panagopulos M., Gray J.E., Hetherington A.M.;
RT "Involvement of sphingosine kinase in plant cell signalling.";
RL Plant J. 56:64-72(2008).
RN [6]
RP SUBCELLULAR LOCATION.
RX PubMed=18643979; DOI=10.1111/j.1365-313x.2008.03596.x;
RA Marion J., Bach L., Bellec Y., Meyer C., Gissot L., Faure J.D.;
RT "Systematic analysis of protein subcellular localization and interaction
RT using high-throughput transient transformation of Arabidopsis seedlings.";
RL Plant J. 56:169-179(2008).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=21330371; DOI=10.1074/jbc.m110.190892;
RA Guo L., Mishra G., Taylor K., Wang X.;
RT "Phosphatidic acid binds and stimulates Arabidopsis sphingosine kinases.";
RL J. Biol. Chem. 286:13336-13345(2011).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=22275366; DOI=10.1074/jbc.m111.274274;
RA Guo L., Mishra G., Markham J.E., Li M., Tawfall A., Welti R., Wang X.;
RT "Connections between sphingosine kinase and phospholipase D in the abscisic
RT acid signaling pathway in Arabidopsis.";
RL J. Biol. Chem. 287:8286-8296(2012).
CC -!- FUNCTION: Involved in the production of sphingolipid metabolites.
CC Phosphorylates sphingosine and various sphingoid long-chain base (LCB)
CC products, such as phytosphingosine (PHS, 4-hydroxysphinganine), 4-
CC hydroxy-8-sphingenine, 4,8-sphingadienine, D-erythro-dihydrosphingosine
CC and D,L-threo-dihydrosphingosine. Is required for abscisic acid (ABA)
CC signaling that mediates stomatal closure, inhibition of seed
CC germination and root elongation. May function upstream of PLDALPHA1 and
CC phosphatidic acid (PA) in an amplification response to ABA that
CC mediates stomatal closure. {ECO:0000269|PubMed:18557834,
CC ECO:0000269|PubMed:21330371, ECO:0000269|PubMed:22275366}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a sphingoid base + ATP = a sphingoid 1-phosphate + ADP + H(+);
CC Xref=Rhea:RHEA:51496, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:76941, ChEBI:CHEBI:84410, ChEBI:CHEBI:456216;
CC EC=2.7.1.91; Evidence={ECO:0000269|PubMed:21330371};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- ACTIVITY REGULATION: Activated by phosphatidic acid (PA). Binding with
CC PA stimulates the activity by promoting the binding of substrate to the
CC catalytic site. {ECO:0000269|PubMed:21330371}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=55 uM for phytosphingosine {ECO:0000269|PubMed:21330371};
CC Vmax=12.94 nmol/min/mg enzyme toward phytosphingosine
CC {ECO:0000269|PubMed:21330371};
CC -!- SUBCELLULAR LOCATION: Vacuole membrane {ECO:0000305|PubMed:18643979,
CC ECO:0000305|PubMed:21330371}; Peripheral membrane protein
CC {ECO:0000305|PubMed:18643979, ECO:0000305|PubMed:21330371}.
CC Note=Associated with the tonoplast.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8L7L1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8L7L1-2; Sequence=VSP_046412, VSP_046413;
CC -!- TISSUE SPECIFICITY: Highly expressed in stems and flowers and at lower
CC levels in roots, leaves and siliques. {ECO:0000269|PubMed:21330371}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions, but seeds have increased germination speed after
CC imbibition, without affecting overall germination rate.
CC {ECO:0000269|PubMed:18557834, ECO:0000269|PubMed:22275366}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AEE84466.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAA18718.1; Type=Erroneous gene model prediction; Note=The predicted gene At4g21540 has been split into 2 genes: At4g21534 and At4g21540.; Evidence={ECO:0000305};
CC Sequence=CAB81261.1; Type=Erroneous gene model prediction; Note=The predicted gene At4g21540 has been split into 2 genes: At4g21534 and At4g21540.; Evidence={ECO:0000305};
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DR EMBL; AL022603; CAA18718.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161555; CAB81261.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE84466.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AY128394; AAM91597.1; -; mRNA.
DR EMBL; BT006621; AAP31965.1; -; mRNA.
DR EMBL; BX826867; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; T05162; T05162.
DR RefSeq; NP_001320022.1; NM_001341496.1.
DR RefSeq; NP_193885.6; NM_118274.8. [Q8L7L1-1]
DR AlphaFoldDB; Q8L7L1; -.
DR SMR; Q8L7L1; -.
DR STRING; 3702.AT4G21540.1; -.
DR iPTMnet; Q8L7L1; -.
DR SwissPalm; Q8L7L1; -.
DR PaxDb; Q8L7L1; -.
DR PRIDE; Q8L7L1; -.
DR ProteomicsDB; 232526; -. [Q8L7L1-1]
DR EnsemblPlants; AT4G21540.1; AT4G21540.1; AT4G21540. [Q8L7L1-1]
DR GeneID; 828239; -.
DR Gramene; AT4G21540.1; AT4G21540.1; AT4G21540. [Q8L7L1-1]
DR KEGG; ath:AT4G21540; -.
DR Araport; AT4G21540; -.
DR TAIR; locus:2119642; AT4G21540.
DR eggNOG; KOG1116; Eukaryota.
DR HOGENOM; CLU_013399_1_2_1; -.
DR InParanoid; Q8L7L1; -.
DR OMA; AECDLGT; -.
DR PhylomeDB; Q8L7L1; -.
DR BioCyc; ARA:AT4G21540-MON; -.
DR BioCyc; MetaCyc:AT4G21540-MON; -.
DR SABIO-RK; Q8L7L1; -.
DR PRO; PR:Q8L7L1; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8L7L1; baseline and differential.
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:0000325; C:plant-type vacuole; HDA:TAIR.
DR GO; GO:0009705; C:plant-type vacuole membrane; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0017050; F:D-erythro-sphingosine kinase activity; IDA:TAIR.
DR GO; GO:0001727; F:lipid kinase activity; IBA:GO_Central.
DR GO; GO:0003951; F:NAD+ kinase activity; IEA:InterPro.
DR GO; GO:0008481; F:sphinganine kinase activity; IDA:UniProtKB.
DR GO; GO:0071215; P:cellular response to abscisic acid stimulus; IMP:UniProtKB.
DR GO; GO:0016310; P:phosphorylation; IBA:GO_Central.
DR GO; GO:0009737; P:response to abscisic acid; IMP:TAIR.
DR GO; GO:0009845; P:seed germination; IMP:TAIR.
DR GO; GO:0006665; P:sphingolipid metabolic process; IDA:UniProtKB.
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; Membrane; Nucleotide-binding;
KW Reference proteome; Stress response; Transferase; Vacuole.
FT CHAIN 1..485
FT /note="Sphingosine kinase 1"
FT /id="PRO_0000422116"
FT DOMAIN 116..258
FT /note="DAGKc"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT ACT_SITE 185
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q9NYA1"
FT BINDING 126..128
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 158
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 183..186
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9NYA1"
FT BINDING 190
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 215..217
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 276
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 283
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 289
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT BINDING 446..448
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00783"
FT VAR_SEQ 288..320
FT /note="ARFDIYGLQRIICLRQYHGRILFVPAPGFESYG -> SEDNMLKTIPWTNSI
FT CASSWVRKLWATSQLQYR (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_046412"
FT VAR_SEQ 321..485
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_046413"
SQ SEQUENCE 485 AA; 53699 MW; 3FFE99FA6DACED5F CRC64;
MDRQPEREND ELPSPAIISD RVLVNGVVTP LTLTAEGELR STESGRRKST LAKEILSFVV
EGNKVRVKTL VEKGGGICCR GSAGDYARND FVFEPLSDES RKLWSDKFHQ HLVSLGRPKK
LLVFVNPFGG KKTARKIFQE EVKPLFEDAN IQLEIQETKY QLHAKEIVRS MDVSKYDGIV
CVSGDGILVE VVNGLLERED WKTAIKLPIG MVPAGSGNGM IKSLLEPVGL PCSATSATIS
IIRGRTRSLD VATISQGTTK FFSVLMLAWG LVADIDIESE KFRWMGSARF DIYGLQRIIC
LRQYHGRILF VPAPGFESYG QRASCSIDKE PSGSDKTLVY QGPDSKLENL DWREMKGPFV
SVWLHNVPWG AENTLAAPDA KFSDGFLDLI VMKDCPKLAL LSLMTKLSDG THVQSPYASY
LKVKAFVLEP GARIDEPDKE GIIDSDGEVL ARGRKSYKCD QKALMSYDKL QISVDQGLAT
LFSPE
