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Q9M304

- LCB2B_ARATH

UniProt

Q9M304 - LCB2B_ARATH

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Protein
Long chain base biosynthesis protein 2b
Gene
LCB2b, LCB2.2, SPT1, At3g48780, T21J18_50
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1 constitutes the catalytic core. Plays an important role during male gametogenesis and embryogenesis.1 Publication

Catalytic activityi

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

Cofactori

Pyridoxal phosphate By similarity.

Pathwayi

GO - Molecular functioni

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

GO - Biological processi

  1. photomorphogenesis Source: TAIR
  2. pollen development Source: TAIR
  3. sphingolipid biosynthetic process Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Lipid metabolism, Sphingolipid metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciARA:AT3G48780-MONOMER.
ReactomeiREACT_190876. Sphingolipid de novo biosynthesis.
UniPathwayiUPA00222.

Names & Taxonomyi

Protein namesi
Recommended name:
Long chain base biosynthesis protein 2b (EC:2.3.1.50)
Short name:
AtLCB2b
Alternative name(s):
Serine palmitoyltransferase 1
Short name:
AtSPT1
Gene namesi
Name:LCB2b
Synonyms:LCB2.2, SPT1
Ordered Locus Names:At3g48780
ORF Names:T21J18_50
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 3

Organism-specific databases

TAIRiAT3G48780.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei2 – 2221Helical; Reviewed prediction
Add
BLAST

GO - Cellular componenti

  1. endoplasmic reticulum membrane Source: UniProtKB-SubCell
  2. integral component of membrane Source: UniProtKB-KW
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 2b
PRO_0000419146Add
BLAST

Amino acid modifications

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

Proteomic databases

PRIDEiQ9M304.

Expressioni

Tissue specificityi

Ubiquitous with the highest expression in flowers.1 Publication

Developmental stagei

In young flower buds was initially restricted to developing pollen spores within the stamen and is not detected in the petals, glumes or petiole until the flowers are mature.1 Publication

Gene expression databases

GenevestigatoriQ9M304.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi3702.AT3G48780.1-P.

Structurei

3D structure databases

ProteinModelPortaliQ9M304.
SMRiQ9M304. Positions 69-469.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

HOGENOMiHOG000206826.
InParanoidiQ9M304.
KOiK00654.
OMAiCADASEE.
PhylomeDBiQ9M304.

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.

Q9M304-1 [UniParc]FASTAAdd to Basket

« Hide

MITIPYLTAV STYFSYGLLF AFGQLRDYSR LIFDWWRTNN LQGYAPICLA    50
HEDFYIRRLY HRIQDCFGRP ISSAPDAWID VVERVSDDNN KTLKRTTKTS 100
RCLNLGSYNY LGFGSFDEYC TPRVIESLKK FSASTCSSRV DAGTTSVHAE 150
LEDCVAKYVG QPAAVIFGMG YATNSAIIPV LIGKGGLIIS DSLNHTSIVN 200
GARGSGATIR VFQHNTPGHL EKVLKEQIAE GQPRTHRPWK KIIVVVEGIY 250
SMEGEICHLP EIVSICKKYK AYVYLDEAHS IGAIGKTGRG VCELLGVDTS 300
DVDIMMGTFT KSFGSCGGYI AGSKDLIQYL KHQCPAHLYA TSISTPSATQ 350
IISAIKVILG EDGSNRGAQK LARIRENSNF FRAELQKMGF EVLGDNDSPV 400
MPIMLYNPAK IPAFSRECLR ENLAVVVVGF PATPLLLARA RICISASHSR 450
EDLIKALQVI SKAGDLTGIK YFPAAPKKQE VEKNGIKLD 489
Length:489
Mass (Da):53,863
Last modified:October 1, 2000 - v1
Checksum:iBE059A00F5632105
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB074928 mRNA. Translation: BAB78461.1.
AL132963 Genomic DNA. Translation: CAB87906.1.
CP002686 Genomic DNA. Translation: AEE78455.1.
AY054489 mRNA. Translation: AAK96680.1.
AY059882 mRNA. Translation: AAL24364.1.
AY114662 mRNA. Translation: AAM47981.1.
BT006615 mRNA. Translation: AAP31959.1.
AK229667 mRNA. Translation: BAF01511.1.
PIRiT49274.
RefSeqiNP_190447.1. NM_114737.4.
UniGeneiAt.1379.
At.75040.

Genome annotation databases

EnsemblPlantsiAT3G48780.1; AT3G48780.1; AT3G48780.
GeneIDi824039.
KEGGiath:AT3G48780.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB074928 mRNA. Translation: BAB78461.1 .
AL132963 Genomic DNA. Translation: CAB87906.1 .
CP002686 Genomic DNA. Translation: AEE78455.1 .
AY054489 mRNA. Translation: AAK96680.1 .
AY059882 mRNA. Translation: AAL24364.1 .
AY114662 mRNA. Translation: AAM47981.1 .
BT006615 mRNA. Translation: AAP31959.1 .
AK229667 mRNA. Translation: BAF01511.1 .
PIRi T49274.
RefSeqi NP_190447.1. NM_114737.4.
UniGenei At.1379.
At.75040.

3D structure databases

ProteinModelPortali Q9M304.
SMRi Q9M304. Positions 69-469.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 3702.AT3G48780.1-P.

Proteomic databases

PRIDEi Q9M304.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT3G48780.1 ; AT3G48780.1 ; AT3G48780 .
GeneIDi 824039.
KEGGi ath:AT3G48780.

Organism-specific databases

TAIRi AT3G48780.

Phylogenomic databases

HOGENOMi HOG000206826.
InParanoidi Q9M304.
KOi K00654.
OMAi CADASEE.
PhylomeDBi Q9M304.

Enzyme and pathway databases

UniPathwayi UPA00222 .
BioCyci ARA:AT3G48780-MONOMER.
Reactomei REACT_190876. Sphingolipid de novo biosynthesis.

Miscellaneous databases

PROi Q9M304.

Gene expression databases

Genevestigatori Q9M304.

Family and domain databases

Gene3Di 3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProi IPR001917. 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 ]
Pfami PF00155. Aminotran_1_2. 1 hit.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 1 hit.
PROSITEi PS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "A gene for serine palmitoyltransferase in Arabidopsis."
    Matsumura M., Mori J., Imai H.
    Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
    Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
    , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "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.
  5. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 244-489.
    Strain: cv. Columbia.
  6. "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.

Entry informationi

Entry nameiLCB2B_ARATH
AccessioniPrimary (citable) accession number: Q9M304
Secondary accession number(s): Q0WMY9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: October 1, 2000
Last modified: September 3, 2014
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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

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