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Protein

Long chain base biosynthesis protein 2a

Gene

LCB2a

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

Functioni

Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1 constitutes the catalytic core. Involved in the regulation of the programmed cell death (PCD) signaling pathway. Plays an important role during male gametogenesis and embryogenesis.3 Publications

Catalytic activityi

Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2.

Cofactori

Pathway:isphingolipid metabolism

This protein is involved in the pathway sphingolipid metabolism, which is part of Lipid metabolism.
View all proteins of this organism that are known to be involved in the pathway sphingolipid metabolism and in Lipid metabolism.

GO - Molecular functioni

  • pyridoxal phosphate binding Source: InterPro
  • serine C-palmitoyltransferase activity Source: TAIR

GO - Biological processi

  • photomorphogenesis Source: TAIR
  • pollen development Source: TAIR
  • regulation of programmed cell death Source: UniProtKB
  • sphingosine biosynthetic process Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Apoptosis, Lipid metabolism, Sphingolipid metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciARA:AT5G23670-MONOMER.
ARA:GQT-1061-MONOMER.
MetaCyc:AT5G23670-MONOMER.
BRENDAi2.3.1.50. 399.
ReactomeiREACT_291245. Sphingolipid de novo biosynthesis.
UniPathwayiUPA00222.

Names & Taxonomyi

Protein namesi
Recommended name:
Long chain base biosynthesis protein 2a (EC:2.3.1.50)
Short name:
AtLCB2a
Alternative name(s):
Long chain base biosynthesis protein 2
Short name:
AtLCB2
Gene namesi
Name:LCB2a
Synonyms:LCB2
Ordered Locus Names:At5g23670
ORF Names:MQM1.6
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G23670.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei2 – 2221HelicalSequence AnalysisAdd
BLAST

GO - Cellular componenti

  • endoplasmic reticulum Source: TAIR
  • endoplasmic reticulum membrane Source: UniProtKB-SubCell
  • integral component of membrane Source: UniProtKB-KW
  • membrane Source: TAIR
  • vacuole Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Disruption phenotypei

No visible phenotype. Lcb2a and lcb2b double mutant is not viable due to pollen lethality.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 489489Long chain base biosynthesis protein 2aPRO_0000419145Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei311 – 3111N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

PRIDEiQ9LSZ9.

Expressioni

Tissue specificityi

Ubiquitous. Detected in leaves, roots, stems, flowers and at a lower level in mature seeds.3 Publications

Developmental stagei

Detected at high levels in the petiole, sepals and petals in young flowers, but was not detected in the anthers during the early stages of pollen development.1 Publication

Interactioni

Subunit structurei

Heterodimer with LCB1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2 (LCB2a or LCB2b).2 Publications

Protein-protein interaction databases

BioGridi17707. 1 interaction.
STRINGi3702.AT5G23670.1.

Structurei

3D structure databases

ProteinModelPortaliQ9LSZ9.
SMRiQ9LSZ9. Positions 62-469.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
HOGENOMiHOG000206826.
InParanoidiQ9LSZ9.
KOiK00654.
OMAiGRELECI.
PhylomeDBiQ9LSZ9.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR001917. Aminotrans_II_pyridoxalP_BS.
IPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9LSZ9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MITIPYLTAV STYFSYGLLF AFGQLRDFFR RFIDWWFTSN LQGYAPICLG
60 70 80 90 100
HEDFYIRRLY HRIQDCFERP ISSAPDAWFD VVERYSNDNN KTLKRTTKTS
110 120 130 140 150
RCLNLGSYNY LGFGSFDEYC TPRVIESLKK FSASTCSSRV DAGTTSVHAE
160 170 180 190 200
LEECVTRFVG KPAAVVFGMG YATNSAIIPV LIGKGGLIIS DSLNHSSIVN
210 220 230 240 250
GARGSGATIR VFQHNTPSHL ERVLREQIAE GQPRTHRPWK KIIVVVEGIY
260 270 280 290 300
SMEGEICHLP EVVAICKKYK AYVYLDEAHS IGAIGKTGKG ICELLGVDTA
310 320 330 340 350
DVDVMMGTFT KSFGSCGGYI AGSKELIQYL KHQCPAHLYA TSIPTPSAQQ
360 370 380 390 400
IISAIKVILG EDGSNRGAQK LARIRENSNF FRAELQKMGF EVLGDNDSPV
410 420 430 440 450
MPIMLYNPAK IPAFSRECLR QKVAVVVVGF PATPLLLARA RICISASHSR
460 470 480
EDLIRALKVI SKVGDLSGIK YFPAEPKKIE QSKNDIKLD
Length:489
Mass (Da):54,290
Last modified:October 1, 2000 - v1
Checksum:i00B396BB47D2E048
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti65 – 651D → N (PubMed:11171191).Curated
Sequence conflicti65 – 651D → N in BAB03231 (PubMed:11726713).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB046384 mRNA. Translation: BAB03231.1.
AB025633 Genomic DNA. Translation: BAA97234.1.
CP002688 Genomic DNA. Translation: AED93196.1.
CP002688 Genomic DNA. Translation: AED93197.1.
AY050829 mRNA. Translation: AAK92764.1.
AY133827 mRNA. Translation: AAM91761.1.
AK316942 mRNA. Translation: BAH19645.1.
RefSeqiNP_001031932.1. NM_001036855.1.
NP_197756.1. NM_122272.3.
UniGeneiAt.23395.
At.49054.

Genome annotation databases

EnsemblPlantsiAT5G23670.1; AT5G23670.1; AT5G23670.
AT5G23670.2; AT5G23670.2; AT5G23670.
GeneIDi832432.
KEGGiath:AT5G23670.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB046384 mRNA. Translation: BAB03231.1.
AB025633 Genomic DNA. Translation: BAA97234.1.
CP002688 Genomic DNA. Translation: AED93196.1.
CP002688 Genomic DNA. Translation: AED93197.1.
AY050829 mRNA. Translation: AAK92764.1.
AY133827 mRNA. Translation: AAM91761.1.
AK316942 mRNA. Translation: BAH19645.1.
RefSeqiNP_001031932.1. NM_001036855.1.
NP_197756.1. NM_122272.3.
UniGeneiAt.23395.
At.49054.

3D structure databases

ProteinModelPortaliQ9LSZ9.
SMRiQ9LSZ9. Positions 62-469.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi17707. 1 interaction.
STRINGi3702.AT5G23670.1.

Proteomic databases

PRIDEiQ9LSZ9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G23670.1; AT5G23670.1; AT5G23670.
AT5G23670.2; AT5G23670.2; AT5G23670.
GeneIDi832432.
KEGGiath:AT5G23670.

Organism-specific databases

TAIRiAT5G23670.

Phylogenomic databases

eggNOGiCOG0156.
HOGENOMiHOG000206826.
InParanoidiQ9LSZ9.
KOiK00654.
OMAiGRELECI.
PhylomeDBiQ9LSZ9.

Enzyme and pathway databases

UniPathwayiUPA00222.
BioCyciARA:AT5G23670-MONOMER.
ARA:GQT-1061-MONOMER.
MetaCyc:AT5G23670-MONOMER.
BRENDAi2.3.1.50. 399.
ReactomeiREACT_291245. Sphingolipid de novo biosynthesis.

Miscellaneous databases

PROiQ9LSZ9.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR001917. Aminotrans_II_pyridoxalP_BS.
IPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterization of a cDNA encoding serine palmitoyltransferase in Arabidopsis thaliana."
    Tamura K., Nishiura H., Mori J., Imai H.
    Biochem. Soc. Trans. 28:745-747(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
  2. "Characterization of an Arabidopsis cDNA encoding a subunit of serine palmitoyltransferase, the initial enzyme in sphingolipid biosynthesis."
    Tamura K., Mitsuhashi N., Hara-Nishimura I., Imai H.
    Plant Cell Physiol. 42:1274-1281(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
  3. "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones."
    Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H., Tabata S.
    DNA Res. 7:31-63(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
    Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
    DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 248-489.
    Strain: cv. Columbia.
    Tissue: Rosette leaf.
  7. "The essential nature of sphingolipids in plants as revealed by the functional identification and characterization of the Arabidopsis LCB1 subunit of serine palmitoyltransferase."
    Chen M., Han G., Dietrich C.R., Dunn T.M., Cahoon E.B.
    Plant Cell 18:3576-3593(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  8. "Loss-of-function mutations and inducible RNAi suppression of Arabidopsis LCB2 genes reveal the critical role of sphingolipids in gametophytic and sporophytic cell viability."
    Dietrich C.R., Han G., Chen M., Berg R.H., Dunn T.M., Cahoon E.B.
    Plant J. 54:284-298(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, SUBUNIT.
  9. "MPK6, sphinganine and the LCB2a gene from serine palmitoyltransferase are required in the signaling pathway that mediates cell death induced by long chain bases in Arabidopsis."
    Saucedo-Garcia M., Guevara-Garcia A., Gonzalez-Solis A., Cruz-Garcia F., Vazquez-Santana S., Markham J.E., Lozano-Rosas M.G., Dietrich C.R., Ramos-Vega M., Cahoon E.B., Gavilanes-Ruiz M.
    New Phytol. 191:943-957(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiLCB2A_ARATH
AccessioniPrimary (citable) accession number: Q9LSZ9
Secondary accession number(s): B9DFX8, Q9LRB4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: October 1, 2000
Last modified: July 22, 2015
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

The lcb2a-1 mutant is incapable of initiating programmed cell death (PCD) after induction by fumonisin B1 (FB1), a specific inhibitor of ceramide synthase.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.