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Q9LSZ9 (LCB2A_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Long chain base biosynthesis protein 2a

Short name=AtLCB2a
EC=2.3.1.50
Alternative name(s):
Long chain base biosynthesis protein 2
Short name=AtLCB2
Gene names
Name:LCB2a
Synonyms:LCB2
Ordered Locus Names:At5g23670
ORF Names:MQM1.6
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length489 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.8 Ref.9

Catalytic activity

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

Cofactor

Pyridoxal phosphate By similarity.

Pathway

Lipid metabolism; sphingolipid metabolism.

Subunit structure

Heterodimer with LCB1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2 (LCB2a or LCB2b). Ref.7 Ref.8

Subcellular location

Endoplasmic reticulum membrane; Single-pass membrane protein Ref.2.

Tissue specificity

Ubiquitous. Detected in leaves, roots, stems, flowers and at a lower level in mature seeds. Ref.1 Ref.2 Ref.8

Developmental stage

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. Ref.8

Disruption phenotype

No visible phenotype. Lcb2a and lcb2b double mutant is not viable due to pollen lethality. Ref.8

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.

Sequence similarities

Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 489489Long chain base biosynthesis protein 2a
PRO_0000419145

Regions

Transmembrane2 – 2221Helical; Potential

Amino acid modifications

Modified residue3111N6-(pyridoxal phosphate)lysine By similarity

Experimental info

Sequence conflict651D → N Ref.1
Sequence conflict651D → N in BAB03231. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Q9LSZ9 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: 00B396BB47D2E048

FASTA48954,290
        10         20         30         40         50         60 
MITIPYLTAV STYFSYGLLF AFGQLRDFFR RFIDWWFTSN LQGYAPICLG HEDFYIRRLY 

        70         80         90        100        110        120 
HRIQDCFERP ISSAPDAWFD VVERYSNDNN KTLKRTTKTS RCLNLGSYNY LGFGSFDEYC 

       130        140        150        160        170        180 
TPRVIESLKK FSASTCSSRV DAGTTSVHAE LEECVTRFVG KPAAVVFGMG YATNSAIIPV 

       190        200        210        220        230        240 
LIGKGGLIIS DSLNHSSIVN GARGSGATIR VFQHNTPSHL ERVLREQIAE GQPRTHRPWK 

       250        260        270        280        290        300 
KIIVVVEGIY SMEGEICHLP EVVAICKKYK AYVYLDEAHS IGAIGKTGKG ICELLGVDTA 

       310        320        330        340        350        360 
DVDVMMGTFT KSFGSCGGYI AGSKELIQYL KHQCPAHLYA TSIPTPSAQQ IISAIKVILG 

       370        380        390        400        410        420 
EDGSNRGAQK LARIRENSNF FRAELQKMGF EVLGDNDSPV MPIMLYNPAK IPAFSRECLR 

       430        440        450        460        470        480 
QKVAVVVVGF PATPLLLARA RICISASHSR EDLIRALKVI SKVGDLSGIK YFPAEPKKIE 


QSKNDIKLD 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001031932.1. NM_001036855.1.
NP_197756.1. NM_122272.3.
UniGeneAt.23395.
At.49054.

3D structure databases

ProteinModelPortalQ9LSZ9.
SMRQ9LSZ9. Positions 62-469.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING3702.AT5G23670.2-P.

Proteomic databases

PRIDEQ9LSZ9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G23670.1; AT5G23670.1; AT5G23670.
AT5G23670.2; AT5G23670.2; AT5G23670.
GeneID832432.
KEGGath:AT5G23670.

Organism-specific databases

TAIRAT5G23670.

Phylogenomic databases

eggNOGCOG0156.
HOGENOMHOG000206826.
InParanoidQ9LSZ9.
KOK00654.
OMAICLGHED.
PhylomeDBQ9LSZ9.

Enzyme and pathway databases

BioCycARA:AT5G23670-MONOMER.
ARA:GQT-1061-MONOMER.
MetaCyc:AT5G23670-MONOMER.
BRENDA2.3.1.50. 302.
UniPathwayUPA00222.

Gene expression databases

GenevestigatorQ9LSZ9.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProIPR001917. 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]
PfamPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMSSF53383. SSF53383. 1 hit.
PROSITEPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROQ9LSZ9.

Entry information

Entry nameLCB2A_ARATH
AccessionPrimary (citable) accession number: Q9LSZ9
Secondary accession number(s): B9DFX8, Q9LRB4
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: October 1, 2000
Last modified: June 11, 2014
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names