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Sphingoid long chain base kinase 4 (LCB kinase 4) (EC 2.7.1.91) (Sphinganine kinase 4)

 LCB4_YEAST              Reviewed;         624 AA.
Q12246; D6W2M7;
31-OCT-2006, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
05-DEC-2018, entry version 151.
RecName: Full=Sphingoid long chain base kinase 4 {ECO:0000303|PubMed:9677363};
Short=LCB kinase 4 {ECO:0000303|PubMed:9677363};
EC=2.7.1.91 {ECO:0000269|PubMed:9677363};
AltName: Full=Sphinganine kinase 4 {ECO:0000305};
Name=LCB4 {ECO:0000303|PubMed:9677363};
OrderedLocusNames=YOR171C {ECO:0000312|SGD:S000005697};
ORFNames=O3615;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 96604 / S288c / FY1679;
PubMed=8972579;
DOI=10.1002/(SICI)1097-0061(199612)12:15<1563::AID-YEA44>3.0.CO;2-M;
Madania A., Poch O., Tarassov I.A., Winsor B., Martin R.P.;
"Analysis of a 22,956 bp region on the right arm of Saccharomyces
cerevisiae chromosome XV.";
Yeast 12:1563-1573(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169874;
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W.,
Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R.,
Boyer J., Camasses A., Casamayor A., Casas C., Cheret G.,
Cziepluch C., Daignan-Fornier B., Dang V.-D., de Haan M., Delius H.,
Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F.,
Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A.,
Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J.,
Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P.,
Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M.,
Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R.,
Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S.,
Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A.,
Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M.,
Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C.,
Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S.,
Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
Nature 387:98-102(1997).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=9677363; DOI=10.1074/jbc.273.31.19437;
Nagiec M.M., Skrzypek M.S., Nagiec E.E., Lester R.L., Dickson R.C.;
"The LCB4 (YOR171c) and LCB5 (YLR260w) genes of Saccharomyces encode
sphingoid long chain base kinases.";
J. Biol. Chem. 273:19437-19442(1998).
[5]
FUNCTION.
PubMed=11102354;
Kim S., Fyrst H., Saba J.D.;
"Accumulation of phosphorylated sphingoid long chain bases results in
cell growth inhibition in Saccharomyces cerevisiae.";
Genetics 156:1519-1529(2000).
[6]
FUNCTION.
PubMed=11795842; DOI=10.1007/s00294-001-0259-6;
Zhang X., Skrzypek M.S., Lester R.L., Dickson R.C.;
"Elevation of endogenous sphingolipid long-chain base phosphates kills
Saccharomyces cerevisiae cells.";
Curr. Genet. 40:221-233(2001).
[7]
FUNCTION.
PubMed=11056159; DOI=10.1074/jbc.M007425200;
Jenkins G.M., Hannun Y.A.;
"Role for de novo sphingoid base biosynthesis in the heat-induced
transient cell cycle arrest of Saccharomyces cerevisiae.";
J. Biol. Chem. 276:8574-8581(2001).
[8]
FUNCTION.
PubMed=11278643; DOI=10.1074/jbc.M010221200;
Birchwood C.J., Saba J.D., Dickson R.C., Cunningham K.W.;
"Calcium influx and signaling in yeast stimulated by intracellular
sphingosine 1-phosphate accumulation.";
J. Biol. Chem. 276:11712-11718(2001).
[9]
SUBCELLULAR LOCATION.
PubMed=12459470; DOI=10.1016/S0014-5793(02)03636-0;
Hait N.C., Fujita K., Lester R.L., Dickson R.C.;
"Lcb4p sphingoid base kinase localizes to the Golgi and late
endosomes.";
FEBS Lett. 532:97-102(2002).
[10]
FUNCTION.
PubMed=11967828; DOI=10.1002/yea.861;
Ferguson-Yankey S.R., Skrzypek M.S., Lester R.L., Dickson R.C.;
"Mutant analysis reveals complex regulation of sphingolipid long chain
base phosphates and long chain bases during heat stress in yeast.";
Yeast 19:573-586(2002).
[11]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=12493772; DOI=10.1074/jbc.M209925200;
Funato K., Lombardi R., Vallee B., Riezman H.;
"Lcb4p is a key regulator of ceramide synthesis from exogenous long
chain sphingoid base in Saccharomyces cerevisiae.";
J. Biol. Chem. 278:7325-7334(2003).
[12]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[13]
PHOSPHORYLATION AT SER-451 AND SER-455, AND UBIQUITINATION.
PubMed=15598647; DOI=10.1074/jbc.M410908200;
Iwaki S., Kihara A., Sano T., Igarashi Y.;
"Phosphorylation by Pho85 cyclin-dependent kinase acts as a signal for
the down-regulation of the yeast sphingoid long-chain base kinase Lcb4
during the stationary phase.";
J. Biol. Chem. 280:6520-6527(2005).
[14]
FUNCTION, PHOSPHORYLATION, AND SUBCELLULAR LOCATION.
PubMed=16141212; DOI=10.1074/jbc.M503147200;
Sano T., Kihara A., Kurotsu F., Iwaki S., Igarashi Y.;
"Regulation of the sphingoid long-chain base kinase Lcb4p by
ergosterol and heme: studies in phytosphingosine-resistant mutants.";
J. Biol. Chem. 280:36674-36682(2005).
[15]
PALMITOYLATION AT CYS-43 AND CYS-46.
PubMed=16227572; DOI=10.1128/MCB.25.21.9189-9197.2005;
Kihara A., Kurotsu F., Sano T., Iwaki S., Igarashi Y.;
"Long-chain base kinase Lcb4 Is anchored to the membrane through its
palmitoylation by Akr1.";
Mol. Cell. Biol. 25:9189-9197(2005).
[16]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-451; SER-454 AND
SER-455, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[17]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-160, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[18]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-111; SER-120; SER-154;
SER-451; SER-454; SER-455 AND SER-460, AND IDENTIFICATION BY MASS
SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
[19]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22814378; DOI=10.1073/pnas.1210303109;
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
Aldabe R.;
"N-terminal acetylome analyses and functional insights of the N-
terminal acetyltransferase NatB.";
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
[20]
UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-148, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22106047; DOI=10.1002/pmic.201100166;
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
"Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
Proteomics 12:236-240(2012).
-!- FUNCTION: Catalyzes the phosphorylation of the sphingoid long
chain bases dihydrosphingosine (DHS or sphinganine) and
phytosphingosine (PHS) to form dihydrosphingosine 1-phosphate
(DHS-1P) and phytosphingosine 1-phosphate (PHS-1P) respectively
(PubMed:9677363, PubMed:11102354, PubMed:11795842,
PubMed:16141212). Involved in the biosynthesis of sphingolipids
and ceramides (PubMed:12493772). Required with LCB3 for an
effective incorporation of DHS into ceramides through a
phosphorylation-dephosphorylation cycle. Involved in heat-induced
transient cell cycle arrest (PubMed:11056159). Accumulation of
phosphorylated sphingoid long chain bases (LCBPs) stimulates
calcium influx and activates calcineurin signaling
(PubMed:11278643). Involved in heat-stress resistance
(PubMed:11967828). {ECO:0000269|PubMed:11056159,
ECO:0000269|PubMed:11102354, ECO:0000269|PubMed:11278643,
ECO:0000269|PubMed:11795842, ECO:0000269|PubMed:11967828,
ECO:0000269|PubMed:12493772, ECO:0000269|PubMed:16141212,
ECO:0000269|PubMed:9677363}.
-!- CATALYTIC ACTIVITY:
Reaction=a sphingoid base + ATP = a sphingoid 1-phosphate + ADP +
H(+); Xref=Rhea:RHEA:51496, ChEBI:CHEBI:15378,
ChEBI:CHEBI:30616, ChEBI:CHEBI:76941, ChEBI:CHEBI:84410,
ChEBI:CHEBI:456216; EC=2.7.1.91;
Evidence={ECO:0000269|PubMed:9677363};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=7.7 uM for sphinganine {ECO:0000269|PubMed:9677363};
KM=25 uM for ATP {ECO:0000269|PubMed:9677363};
-!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:12459470,
ECO:0000269|PubMed:16141212}; Peripheral membrane protein
{ECO:0000305}. Endoplasmic reticulum membrane
{ECO:0000269|PubMed:12493772}; Peripheral membrane protein
{ECO:0000305}. Late endosome membrane
{ECO:0000269|PubMed:12459470}; Peripheral membrane protein
{ECO:0000305}. Golgi apparatus membrane
{ECO:0000269|PubMed:12459470}; Peripheral membrane protein
{ECO:0000305}.
-!- PTM: Phosphorylated by the cyclin-CDKs PCL1-PHO85 and PCL2-PHO85.
Phosphorylation is a prerequisite to ubiquitination. The
phosphorylation level depends on sterol composition and may also
be involved in subcellular location (PubMed:16141212).
{ECO:0000269|PubMed:15598647, ECO:0000269|PubMed:16141212}.
-!- PTM: Ubiquitinated. The ubiquitination leads to degradation in the
vacuole. {ECO:0000269|PubMed:15598647}.
-!- MISCELLANEOUS: Present with 2840 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
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EMBL; U55021; AAB47416.1; -; Genomic_DNA.
EMBL; Z75078; CAA99378.1; -; Genomic_DNA.
EMBL; BK006948; DAA10943.1; -; Genomic_DNA.
PIR; S67059; S67059.
RefSeq; NP_014814.1; NM_001183590.1.
ProteinModelPortal; Q12246; -.
BioGrid; 34565; 152.
DIP; DIP-2844N; -.
IntAct; Q12246; 3.
MINT; Q12246; -.
STRING; 4932.YOR171C; -.
SwissLipids; SLP:000000109; -.
iPTMnet; Q12246; -.
SwissPalm; Q12246; -.
MaxQB; Q12246; -.
PaxDb; Q12246; -.
PRIDE; Q12246; -.
EnsemblFungi; YOR171C_mRNA; YOR171C_mRNA; YOR171C.
GeneID; 854342; -.
KEGG; sce:YOR171C; -.
SGD; S000005697; LCB4.
GeneTree; ENSGT00940000167991; -.
HOGENOM; HOG000207396; -.
InParanoid; Q12246; -.
KO; K04718; -.
OMA; FYCGNMA; -.
OrthoDB; EOG092C1LMZ; -.
BioCyc; MetaCyc:YOR171C-MONOMER; -.
BioCyc; YEAST:YOR171C-MONOMER; -.
Reactome; R-SCE-1483206; Glycerophospholipid biosynthesis.
Reactome; R-SCE-1660661; Sphingolipid de novo biosynthesis.
Reactome; R-SCE-1660662; Glycosphingolipid metabolism.
Reactome; R-SCE-390471; Association of TriC/CCT with target proteins during biosynthesis.
Reactome; R-SCE-5218921; VEGFR2 mediated cell proliferation.
PRO; PR:Q12246; -.
Proteomes; UP000002311; Chromosome XV.
GO; GO:0032541; C:cortical endoplasmic reticulum; IDA:SGD.
GO; GO:0005783; C:endoplasmic reticulum; IDA:SGD.
GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
GO; GO:0005794; C:Golgi apparatus; IDA:SGD.
GO; GO:0000139; C:Golgi membrane; IEA:UniProtKB-SubCell.
GO; GO:0031902; C:late endosome membrane; IEA:UniProtKB-SubCell.
GO; GO:0005886; C:plasma membrane; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0017050; F:D-erythro-sphingosine kinase activity; IDA:SGD.
GO; GO:0003951; F:NAD+ kinase activity; IEA:InterPro.
GO; GO:0008481; F:sphinganine kinase activity; IEA:UniProtKB-EC.
GO; GO:0019722; P:calcium-mediated signaling; IMP:SGD.
GO; GO:0006665; P:sphingolipid metabolic process; IDA:SGD.
Gene3D; 3.40.50.10330; -; 1.
InterPro; IPR017438; ATP-NAD_kinase_N.
InterPro; IPR001206; Diacylglycerol_kinase_cat_dom.
InterPro; IPR016064; NAD/diacylglycerol_kinase_sf.
Pfam; PF00781; DAGK_cat; 1.
SMART; SM00046; DAGKc; 1.
SUPFAM; SSF111331; SSF111331; 1.
PROSITE; PS50146; DAGK; 1.
1: Evidence at protein level;
ATP-binding; Cell membrane; Complete proteome; Endoplasmic reticulum;
Endosome; Golgi apparatus; Isopeptide bond; Kinase; Lipid metabolism;
Lipoprotein; Membrane; Nucleotide-binding; Palmitate; Phosphoprotein;
Reference proteome; Sphingolipid metabolism; Transferase;
Ubl conjugation.
CHAIN 1 624 Sphingoid long chain base kinase 4.
/FTId=PRO_0000255956.
DOMAIN 224 363 DAGKc. {ECO:0000255|PROSITE-
ProRule:PRU00783}.
NP_BIND 234 236 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00783}.
NP_BIND 324 326 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00783}.
NP_BIND 589 591 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00783}.
REGION 291 294 Substrate binding. {ECO:0000250}.
ACT_SITE 293 293 Proton donor/acceptor. {ECO:0000250}.
BINDING 266 266 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00783}.
BINDING 298 298 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00783}.
BINDING 392 392 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00783}.
BINDING 398 398 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00783}.
MOD_RES 111 111 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 120 120 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 154 154 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 160 160 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
MOD_RES 451 451 Phosphoserine; by PHO85.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:19779198,
ECO:0000269|PubMed:15598647}.
MOD_RES 454 454 Phosphoserine.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:19779198}.
MOD_RES 455 455 Phosphoserine; by PHO85.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:19779198,
ECO:0000269|PubMed:15598647}.
MOD_RES 460 460 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
LIPID 43 43 S-palmitoyl cysteine.
{ECO:0000269|PubMed:16227572}.
LIPID 46 46 S-palmitoyl cysteine.
{ECO:0000269|PubMed:16227572}.
CROSSLNK 148 148 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000244|PubMed:22106047}.
SEQUENCE 624 AA; 69639 MW; E033A3BAC604D4BB CRC64;
MVVQKKLRAI LTDEGVLIKS QSHHMFNKHG QLRSGDSLSL LSCLSCLDDG TLSSDGGSFD
EDDSLELLPL NTTIPFNRIL NAKYVNVGQK GFNNGKISSN PFQTENLSSS SENDDVENHS
LSNDKAPVSE SQSFPKKDKW DTKTNTVKVS PDDSQDNSPS LGIKDNQQLI ELTFAVPKGH
DVIPQKLTLL IDHVSRKSRA NTGEENISSG TVEEILEKSY ENSKRNRSIL VIINPHGGKG
TAKNLFLTKA RPILVESGCK IEIAYTKYAR HAIDIAKDLD ISKYDTIACA SGDGIPYEVI
NGLYRRPDRV DAFNKLAVTQ LPCGSGNAMS ISCHWTNNPS YAALCLVKSI ETRIDLMCCS
QPSYMNEWPR LSFLSQTYGV IAESDINTEF IRWMGPVRFN LGVAFNIIQG KKYPCEVFVK
YAAKSKKELK VHFLENKDKN KGCLTFEPNP SPNSSPDLLS KNNINNSTKD ELSPNFLNED
NFKLKYPMTE PVPRDWEKMD SELTDNLTIF YTGKMPYIAK DTKFFPAALP ADGTIDLVIT
DARIPVTRMT PILLSLDKGS HVLEPEVIHS KILAYKIIPK VESGLFSVDG EKFPLEPLQV
EIMPMLCKTL LRNGRYIDTE FESM


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18-785-210404 SEK1_MKK4 (Phospho-Ser80) - EC 2.7.12.2; MAP kinase kinase 4; JNK-activating kinase 1; c-Jun N-terminal kinase kinase 1; JNKK; SAPK_ERK kinase 1; SEK1 Polyclonal 0.1 mg
18-785-210403 SEK1_MKK4 (Phospho-Thr261) - EC 2.7.12.2; MAP kinase kinase 4; JNK-activating kinase 1; c-Jun N-terminal kinase kinase 1; JNKK; SAPK_ERK kinase 1; SEK1 Polyclonal 0.05 mg
18-785-210403 SEK1_MKK4 (Phospho-Thr261) - EC 2.7.12.2; MAP kinase kinase 4; JNK-activating kinase 1; c-Jun N-terminal kinase kinase 1; JNKK; SAPK_ERK kinase 1; SEK1 Polyclonal 0.1 mg
10-782-55047 Dual specificity mitogen-activated protein kinase kinase 1 - EC 2.7.12.2; MAP kinase kinase 1; MAPKK 1; ERK activator kinase 1; MAPK_ERK kinase 1; MEK1 N_A 0.02 mg
10-782-55048 Dual specificity mitogen-activated protein kinase kinase 1 - EC 2.7.12.2; MAP kinase kinase 1; MAPKK 1; ERK activator kinase 1; MAPK_ERK kinase 1; MEK1 N_A 0.05 mg
18-785-210404 SEK1_MKK4 (Phospho-Ser80) - EC 2.7.12.2; MAP kinase kinase 4; JNK-activating kinase 1; c-Jun N-terminal kinase kinase 1; JNKK; SAPK_ERK kinase 1; SEK1 Polyclonal 0.05 mg


 

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