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Protein

Long chain base biosynthesis protein 2a

Gene

LCB2a

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -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

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.

Catalytic activityi

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

Cofactori

Pathwayi: sphingolipid 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

Keywordsi

Molecular functionAcyltransferase, Transferase
Biological processApoptosis, Lipid metabolism, Sphingolipid metabolism
LigandPyridoxal phosphate

Enzyme and pathway databases

BioCyciARA:AT5G23670-MONOMER
MetaCyc:AT5G23670-MONOMER
BRENDAi2.3.1.50 399
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
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

AraportiAT5G23670
TAIRilocus:2171731 AT5G23670

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei2 – 22HelicalSequence analysisAdd BLAST21

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)DescriptionActionsGraphical viewLength
ChainiPRO_00004191451 – 489Long chain base biosynthesis protein 2aAdd BLAST489

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei311N6-(pyridoxal phosphate)lysineBy similarity1

Proteomic databases

PaxDbiQ9LSZ9

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

Gene expression databases

ExpressionAtlasiQ9LSZ9 baseline and differential
GenevisibleiQ9LSZ9 AT

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 interactor
STRINGi3702.AT5G23670.1

Structurei

3D structure databases

ProteinModelPortaliQ9LSZ9
SMRiQ9LSZ9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG1357 Eukaryota
COG0156 LUCA
HOGENOMiHOG000206826
InParanoidiQ9LSZ9
KOiK00654
OMAiYPVIPKG
OrthoDBiEOG0936074X
PhylomeDBiQ9LSZ9

Family and domain databases

Gene3Di3.40.640.10, 1 hit
3.90.1150.10, 2 hits
InterProiView protein in InterPro
IPR001917 Aminotrans_II_pyridoxalP_BS
IPR004839 Aminotransferase_I/II
IPR015424 PyrdxlP-dep_Trfase
IPR015422 PyrdxlP-dep_Trfase_dom1
IPR015421 PyrdxlP-dep_Trfase_major
PfamiView protein in Pfam
PF00155 Aminotran_1_2, 1 hit
SUPFAMiSSF53383 SSF53383, 1 hit
PROSITEiView protein in PROSITE
PS00599 AA_TRANSFER_CLASS_2, 1 hit

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)DescriptionActionsGraphical viewLength
Sequence conflicti65D → N (PubMed:11171191).Curated1
Sequence conflicti65D → N in BAB03231 (PubMed:11726713).Curated1

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
GrameneiAT5G23670.1; AT5G23670.1; AT5G23670
AT5G23670.2; AT5G23670.2; AT5G23670
KEGGiath:AT5G23670

Similar proteinsi

Entry informationi

Entry nameiLCB2A_ARATH
AccessioniPrimary (citable) accession number: Q9LSZ9
Secondary accession number(s): B9DFX8, Q9LRB4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: October 1, 2000
Last modified: April 25, 2018
This is version 127 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
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health