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Protein

Sphingoid long-chain bases kinase 1

Gene

LCBK1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the production of sphingolipid metabolites. Active on sphingosine, phytosphingosine (PHS, 4-hydroxysphinganine), D-erythro-dihydrosphingosine, D-erythro-sphingosine and trans-4, trans-8-sphingadienine, an LCB found exclusively in plants, but not on N-acetyl-dihydrosphingosine (C2-dihydroceramide) and D-threo-dihydrosphingosine.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei287ATPPROSITE-ProRule annotation1
Active sitei315Proton donor/acceptorBy similarity1
Binding sitei320ATPPROSITE-ProRule annotation1
Binding sitei418ATPPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi255 – 257ATPPROSITE-ProRule annotation3
Nucleotide bindingi345 – 347ATPPROSITE-ProRule annotation3
Nucleotide bindingi733 – 735ATPPROSITE-ProRule annotation3

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • D-erythro-sphingosine kinase activity Source: UniProtKB
  • NAD+ kinase activity Source: InterPro

GO - Biological processi

  • sphingolipid biosynthetic process Source: UniProtKB

Keywordsi

Molecular functionKinase, Transferase
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciARA:AT5G23450-MONOMER.
ReactomeiR-ATH-1483206. Glycerophospholipid biosynthesis.

Names & Taxonomyi

Protein namesi
Recommended name:
Sphingoid long-chain bases kinase 1 (EC:2.7.-.-)
Short name:
AtLCBK1
Short name:
LCB kinase 1
Alternative name(s):
Sphingosine kinase 1
Gene namesi
Name:LCBK1
Ordered Locus Names:At5g23450
ORF Names:K19M13.8
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

AraportiAT5G23450.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003120011 – 763Sphingoid long-chain bases kinase 1Add BLAST763

Proteomic databases

PaxDbiQ9LRB0.

PTM databases

iPTMnetiQ9LRB0.
SwissPalmiQ9LRB0.

Expressioni

Tissue specificityi

Expressed in roots, stems, leaves and at higher levels in flowers.1 Publication

Inductioni

Not induced by low-humidity stress or by abscisic acid treatment.1 Publication

Gene expression databases

ExpressionAtlasiQ9LRB0. baseline and differential.
GenevisibleiQ9LRB0. AT.

Interactioni

Protein-protein interaction databases

BioGridi17686. 3 interactors.
STRINGi3702.AT5G23450.3.

Structurei

3D structure databases

ProteinModelPortaliQ9LRB0.
SMRiQ9LRB0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini245 – 384DAGKcPROSITE-ProRule annotationAdd BLAST140

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni313 – 316Substrate bindingBy similarity4

Phylogenomic databases

eggNOGiKOG1116. Eukaryota.
COG1597. LUCA.
HOGENOMiHOG000243538.
InParanoidiQ9LRB0.
PhylomeDBiQ9LRB0.

Family and domain databases

Gene3Di3.40.50.10330. 1 hit.
InterProiView protein in InterPro
IPR017438. ATP-NAD_kinase_N.
IPR001206. Diacylglycerol_kinase_cat_dom.
IPR016064. NAD/diacylglycerol_kinase_sf.
PfamiView protein in Pfam
PF00781. DAGK_cat. 1 hit.
SMARTiView protein in SMART
SM00046. DAGKc. 1 hit.
SUPFAMiSSF111331. SSF111331. 2 hits.
PROSITEiView protein in PROSITE
PS50146. DAGK. 1 hit.

Sequencei

Sequence statusi: Complete.

This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: Q9LRB0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MQKSGVNRNP SLKVAIPQAQ QSLRRLGFCS QIATGGSQQS SPIVFPEKRN
60 70 80 90 100
KKVKASSRRG EVTNDPQVKP KPDEHRIDIG GGDEKSDLLG SLVYAGKLVL
110 120 130 140 150
DKRKSASGKD ATEIQQPAAT DISIKKAVDA KLTSSALVWG SDMLQLNDVV
160 170 180 190 200
SVTYNVGLRH FTVHAYPIGK GSCGLSCFTK PKRSRKDFRF VAPTVEEAVQ
210 220 230 240 250
WVASFGDQQC FINCLPHPLV AKKQASSELF SVPIDTPPEL VFRCKSAPKM
260 270 280 290 300
LVILNPRSGH GRSIKVFHNV VEPIFKLAGI KMEVVKTTKA GHARELASTV
310 320 330 340 350
DINLCSDGII CVGGDGIINE VLNGLLTRSN PKEGVSIPIG IVPAGSDNSL
360 370 380 390 400
VWTVLGVRDP ISAALSIVKG GLTATDVFAV EWIHTGIIHF GMTVSYYGFV
410 420 430 440 450
SDVLELSEKY QKRFGPLRYF VAGFLKFMCL PKYSYEVEYL PAQKEDAEGK
460 470 480 490 500
IRLEKEAVDM QDLYTDVMRR SSREGFPRAS SLSSIDSIMT PSVGELDTCS
510 520 530 540 550
STHASTEPSE YVRGIDPKMK RLSSGRRDVT AEPEVIHPQA QSTTPNWPRT
560 570 580 590 600
RSKSRMDKGW MGLTSVQDPP TRCSWGNTGG QDREDISSTV SDPGPIWDAG
610 620 630 640 650
PKWDTEPSAW DVENSIELPG PPEDIETGLR KQSITPIFED KWVSRKGHFL
660 670 680 690 700
GIMVCNHACR TVQSSQVVAP NSEHDDGTMD MLLVHGCGRL RLLRFFILLQ
710 720 730 740 750
TGRHLSLPYV ECVKVKSVKI KAGKNTHDSC GIDGELFALH GEVISTMLPE
760
QCRLIGNAPG RHS
Length:763
Mass (Da):83,592
Last modified:October 1, 2000 - v1
Checksum:i870927E419B4277C
GO

Sequence cautioni

The sequence BAB09561 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti22S → P in BAH20145 (PubMed:19423640).Curated1
Sequence conflicti401S → G in BAH20145 (PubMed:19423640).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB046717 mRNA. Translation: BAB07787.1.
AB018110 Genomic DNA. Translation: BAB09561.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED93169.1.
CP002688 Genomic DNA. Translation: AED93170.1.
CP002688 Genomic DNA. Translation: ANM69595.1.
AY139759 mRNA. Translation: AAM98080.1.
BT004544 mRNA. Translation: AAO42790.1.
AK317480 mRNA. Translation: BAH20145.1.
RefSeqiNP_001331261.1. NM_001343804.1. [Q9LRB0-1]
NP_568432.1. NM_122252.4. [Q9LRB0-1]
NP_851065.1. NM_180734.3. [Q9LRB0-1]
UniGeneiAt.22459.

Genome annotation databases

EnsemblPlantsiAT5G23450.1; AT5G23450.1; AT5G23450. [Q9LRB0-1]
AT5G23450.2; AT5G23450.2; AT5G23450. [Q9LRB0-1]
AT5G23450.5; AT5G23450.5; AT5G23450. [Q9LRB0-1]
GeneIDi832411.
GrameneiAT5G23450.1; AT5G23450.1; AT5G23450.
AT5G23450.2; AT5G23450.2; AT5G23450.
AT5G23450.5; AT5G23450.5; AT5G23450.
KEGGiath:AT5G23450.

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiLCBK1_ARATH
AccessioniPrimary (citable) accession number: Q9LRB0
Secondary accession number(s): B9DHC8, Q9FHL3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 4, 2007
Last sequence update: October 1, 2000
Last modified: November 22, 2017
This is version 108 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names