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Q94IB8 (LCB1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 89. 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 1

Short name=AtLCB1
EC=2.3.1.50
Alternative name(s):
Protein EMBRYO DEFECTIVE 2779
Protein FUMONISIN B1 RESISTANT 11
Gene names
Name:LCB1
Synonyms:EMB2779, FBR11
Ordered Locus Names:At4g36480
ORF Names:AP22, C7A10.880
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length482 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Subcellular location

Endoplasmic reticulum membrane; Single-pass membrane protein Ref.7.

Tissue specificity

Ubiquitous. Ref.7

Disruption phenotype

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. Ref.7 Ref.9

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.

Sequence similarities

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

Sequence caution

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

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 482482Long chain base biosynthesis protein 1
PRO_0000419144

Regions

Transmembrane32 – 5221Helical; Potential

Experimental info

Sequence conflict3061K → E in BAH20117. Ref.6

Sequences

Sequence LengthMass (Da)Tools
Q94IB8 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: CE23247C3F7ADE28

FASTA48253,141
        10         20         30         40         50         60 
MASNLVEMFN AALNWVTMIL ESPSARVVLF GVPIRGHFFV EGLLGVVIII LLTRKSYKPP 

        70         80         90        100        110        120 
KRPLTEQEID ELCDEWVPEP LIPPITEDMK HEPPVLESAA GPHTTVNGKD VVNFASANYL 

       130        140        150        160        170        180 
GLIGHEKLLE SCTSALEKYG VGSCGPRGFY GTIDVHLDCE TRISKFLGTP DSILYSYGLS 

       190        200        210        220        230        240 
TMFSTIPCFC KKGDVIVADE GVHWGIQNGL QLSRSTIVYF KHNDMESLRI TLEKIMTKYK 

       250        260        270        280        290        300 
RSKNLRRYIV AEAVYQNSGQ IAPLDEIVKL KEKYRFRVIL DESNSFGVLG RSGRGLAEHH 

       310        320        330        340        350        360 
SVPIEKIDVV TAAMGHALAT EGGFCTGNAR IIDYQRLSSS GYVFSASLPP YLASAAITAI 

       370        380        390        400        410        420 
DVIDQNPDML VKLKQNVALL WKGLSDIKGM SLTSNRESPI VFLKLEKSSG SAKDDLLLLE 

       430        440        450        460        470        480 
KMADRALKED SLLVVSSKRS FLDKCRLPVG IKLYVSAGHS ESDLLKASES LKRLASELLL 


KS 

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References

« Hide 'large scale' references
[1]"Cloning and characterization of a cDNA encoding a subunit of serine palmitoyltransferase."
Mori J., Tamura K., Nishiura H., Morimoto Y., Imai H.
Submitted (JUN-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. expand/collapse author list , 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(1998) [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. expand/collapse author list , 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(1999) [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].
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: 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(2007) [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(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DISRUPTION PHENOTYPE.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRF85430.
RefSeqNP_001031796.1. NM_001036719.1.
NP_568005.1. NM_119811.2.
UniGeneAt.22137.

3D structure databases

ProteinModelPortalQ94IB8.
SMRQ94IB8. Positions 95-478.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ94IB8. 2 interactions.
STRING3702.AT4G36480.2-P.

Proteomic databases

PRIDEQ94IB8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT4G36480.1; AT4G36480.1; AT4G36480.
AT4G36480.2; AT4G36480.2; AT4G36480.
GeneID829800.
KEGGath:AT4G36480.

Organism-specific databases

TAIRAT4G36480.

Phylogenomic databases

eggNOGCOG0156.
HOGENOMHOG000216602.
InParanoidQ94IB8.
KOK00654.
OMATGPPSHK.
PhylomeDBQ94IB8.

Enzyme and pathway databases

BioCycARA:AT4G36480-MONOMER.
ARA:GQT-1717-MONOMER.
MetaCyc:AT4G36480-MONOMER.
UniPathwayUPA00222.

Gene expression databases

GenevestigatorQ94IB8.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
InterProIPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]
PfamPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMSSF53383. SSF53383. 1 hit.
ProtoNetSearch...

Other

PROQ94IB8.

Entry information

Entry nameLCB1_ARATH
AccessionPrimary (citable) accession number: Q94IB8
Secondary accession number(s): B9DHA0, O23233
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: December 1, 2001
Last modified: June 11, 2014
This is version 89 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