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Protein

Long chain base biosynthesis protein 1

Gene

LCB1

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 LCB2 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

Pathwayi

GO - Molecular functioni

  1. pyridoxal phosphate binding Source: InterPro
  2. serine C-palmitoyltransferase activity Source: UniProtKB-EC

GO - Biological processi

  1. apoptotic process Source: UniProtKB-KW
  2. cell growth Source: TAIR
  3. regulation of programmed cell death Source: UniProtKB
  4. sphingolipid 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:AT4G36480-MONOMER.
ARA:GQT-1717-MONOMER.
MetaCyc:AT4G36480-MONOMER.
ReactomeiREACT_291245. Sphingolipid de novo biosynthesis.
UniPathwayiUPA00222.

Names & Taxonomyi

Protein namesi
Recommended name:
Long chain base biosynthesis protein 1 (EC:2.3.1.50)
Short name:
AtLCB1
Alternative name(s):
Protein EMBRYO DEFECTIVE 2779
Protein FUMONISIN B1 RESISTANT 11
Gene namesi
Name:LCB1
Synonyms:EMB2779, FBR11
Ordered Locus Names:At4g36480
ORF Names:AP22, C7A10.880
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G36480.

Subcellular locationi

Endoplasmic reticulum membrane 1 Publication; Single-pass membrane protein 1 Publication

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei32 – 5221HelicalSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. endoplasmic reticulum Source: TAIR
  2. endoplasmic reticulum membrane Source: UniProtKB-SubCell
  3. integral component of membrane Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Disruption phenotypei

Defective Embryo and pollen lethality. RNAi mutants display plant size reduction, altered leaf morphology and increases in relative amounts of saturated sphingolipid long-chain bases.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 482482Long chain base biosynthesis protein 1PRO_0000419144Add
BLAST

Proteomic databases

PRIDEiQ94IB8.

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Gene expression databases

GenevestigatoriQ94IB8.

Interactioni

Subunit structurei

Heterodimer with LCB2 (LCB2a or LCB2b). Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2 (LCB2a or LCB2b).1 Publication

Protein-protein interaction databases

IntActiQ94IB8. 2 interactions.
STRINGi3702.AT4G36480.2-P.

Structurei

3D structure databases

ProteinModelPortaliQ94IB8.
SMRiQ94IB8. Positions 95-478.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
HOGENOMiHOG000216602.
InParanoidiQ94IB8.
KOiK00654.
OMAiFIRYLMA.
PhylomeDBiQ94IB8.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
InterProiIPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.

Sequencei

Sequence statusi: Complete.

Q94IB8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASNLVEMFN AALNWVTMIL ESPSARVVLF GVPIRGHFFV EGLLGVVIII
60 70 80 90 100
LLTRKSYKPP KRPLTEQEID ELCDEWVPEP LIPPITEDMK HEPPVLESAA
110 120 130 140 150
GPHTTVNGKD VVNFASANYL GLIGHEKLLE SCTSALEKYG VGSCGPRGFY
160 170 180 190 200
GTIDVHLDCE TRISKFLGTP DSILYSYGLS TMFSTIPCFC KKGDVIVADE
210 220 230 240 250
GVHWGIQNGL QLSRSTIVYF KHNDMESLRI TLEKIMTKYK RSKNLRRYIV
260 270 280 290 300
AEAVYQNSGQ IAPLDEIVKL KEKYRFRVIL DESNSFGVLG RSGRGLAEHH
310 320 330 340 350
SVPIEKIDVV TAAMGHALAT EGGFCTGNAR IIDYQRLSSS GYVFSASLPP
360 370 380 390 400
YLASAAITAI DVIDQNPDML VKLKQNVALL WKGLSDIKGM SLTSNRESPI
410 420 430 440 450
VFLKLEKSSG SAKDDLLLLE KMADRALKED SLLVVSSKRS FLDKCRLPVG
460 470 480
IKLYVSAGHS ESDLLKASES LKRLASELLL KS
Length:482
Mass (Da):53,141
Last modified:December 1, 2001 - v1
Checksum:iCE23247C3F7ADE28
GO

Sequence cautioni

The sequence CAB16844.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAB80314.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti306 – 3061K → E in BAH20117 (PubMed:19423640).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB063254 mRNA. Translation: BAB60898.1.
Z99708 Genomic DNA. Translation: CAB16844.1. Sequence problems.
AL161589 Genomic DNA. Translation: CAB80314.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE86660.1.
CP002687 Genomic DNA. Translation: AEE86661.1.
AY120759 mRNA. Translation: AAM53317.1.
BT000131 mRNA. Translation: AAN15450.1.
AK317450 mRNA. Translation: BAH20117.1.
PIRiF85430.
RefSeqiNP_001031796.1. NM_001036719.1.
NP_568005.1. NM_119811.2.
UniGeneiAt.22137.

Genome annotation databases

EnsemblPlantsiAT4G36480.1; AT4G36480.1; AT4G36480.
AT4G36480.2; AT4G36480.2; AT4G36480.
GeneIDi829800.
KEGGiath:AT4G36480.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB063254 mRNA. Translation: BAB60898.1.
Z99708 Genomic DNA. Translation: CAB16844.1. Sequence problems.
AL161589 Genomic DNA. Translation: CAB80314.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE86660.1.
CP002687 Genomic DNA. Translation: AEE86661.1.
AY120759 mRNA. Translation: AAM53317.1.
BT000131 mRNA. Translation: AAN15450.1.
AK317450 mRNA. Translation: BAH20117.1.
PIRiF85430.
RefSeqiNP_001031796.1. NM_001036719.1.
NP_568005.1. NM_119811.2.
UniGeneiAt.22137.

3D structure databases

ProteinModelPortaliQ94IB8.
SMRiQ94IB8. Positions 95-478.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ94IB8. 2 interactions.
STRINGi3702.AT4G36480.2-P.

Proteomic databases

PRIDEiQ94IB8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G36480.1; AT4G36480.1; AT4G36480.
AT4G36480.2; AT4G36480.2; AT4G36480.
GeneIDi829800.
KEGGiath:AT4G36480.

Organism-specific databases

TAIRiAT4G36480.

Phylogenomic databases

eggNOGiCOG0156.
HOGENOMiHOG000216602.
InParanoidiQ94IB8.
KOiK00654.
OMAiFIRYLMA.
PhylomeDBiQ94IB8.

Enzyme and pathway databases

UniPathwayiUPA00222.
BioCyciARA:AT4G36480-MONOMER.
ARA:GQT-1717-MONOMER.
MetaCyc:AT4G36480-MONOMER.
ReactomeiREACT_291245. Sphingolipid de novo biosynthesis.

Miscellaneous databases

PROiQ94IB8.

Gene expression databases

GenevestigatoriQ94IB8.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
InterProiIPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterization of a cDNA encoding a subunit of serine palmitoyltransferase."
    Mori J., Tamura K., Nishiura H., Morimoto Y., Imai H.
    Submitted (MAY-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana."
    Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C., Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P., Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.
    , Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R., De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M., Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M., Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A., Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D., Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A., Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S., Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G., Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.
    Nature 391:485-488(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-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(2002) [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(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    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(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, SUBUNIT.
  8. "Involvement of sphingoid bases in mediating reactive oxygen intermediate production and programmed cell death in Arabidopsis."
    Shi L., Bielawski J., Mu J., Dong H., Teng C., Zhang J., Yang X., Tomishige N., Hanada K., Hannun Y.A., Zuo J.
    Cell Res. 17:1030-1040(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Serine palmitoyltransferase, a key enzyme for de novo synthesis of sphingolipids, is essential for male gametophyte development in Arabidopsis."
    Teng C., Dong H., Shi L., Deng Y., Mu J., Zhang J., Yang X., Zuo J.
    Plant Physiol. 146:1322-1332(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiLCB1_ARATH
AccessioniPrimary (citable) accession number: Q94IB8
Secondary accession number(s): B9DHA0, O23233
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: December 1, 2001
Last modified: April 1, 2015
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

The fbr11-1 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.