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Q9M304 (LCB2B_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 97. 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 2b

Short name=AtLCB2b
EC=2.3.1.50
Alternative name(s):
Serine palmitoyltransferase 1
Short name=AtSPT1
Gene names
Name:LCB2b
Synonyms:LCB2.2, SPT1
Ordered Locus Names:At3g48780
ORF Names:T21J18_50
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. Plays an important role during male gametogenesis and embryogenesis. Ref.6

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.6

Subcellular location

Endoplasmic reticulum membrane; Single-pass membrane protein By similarity.

Tissue specificity

Ubiquitous with the highest expression in flowers. Ref.6

Developmental stage

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. Ref.6

Disruption phenotype

No visible phenotype. Lcb2a and lcb2b double mutant is not viable due to pollen lethality. Ref.6

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 2b
PRO_0000419146

Regions

Transmembrane2 – 2221Helical; Potential

Amino acid modifications

Modified residue3111N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q9M304 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: BE059A00F5632105

FASTA48953,863
        10         20         30         40         50         60 
MITIPYLTAV STYFSYGLLF AFGQLRDYSR LIFDWWRTNN LQGYAPICLA HEDFYIRRLY 

        70         80         90        100        110        120 
HRIQDCFGRP ISSAPDAWID VVERVSDDNN KTLKRTTKTS RCLNLGSYNY LGFGSFDEYC 

       130        140        150        160        170        180 
TPRVIESLKK FSASTCSSRV DAGTTSVHAE LEDCVAKYVG QPAAVIFGMG YATNSAIIPV 

       190        200        210        220        230        240 
LIGKGGLIIS DSLNHTSIVN GARGSGATIR VFQHNTPGHL EKVLKEQIAE GQPRTHRPWK 

       250        260        270        280        290        300 
KIIVVVEGIY SMEGEICHLP EIVSICKKYK AYVYLDEAHS IGAIGKTGRG VCELLGVDTS 

       310        320        330        340        350        360 
DVDIMMGTFT KSFGSCGGYI AGSKDLIQYL KHQCPAHLYA TSISTPSATQ IISAIKVILG 

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

       430        440        450        460        470        480 
ENLAVVVVGF PATPLLLARA RICISASHSR EDLIKALQVI SKAGDLTGIK YFPAAPKKQE 


VEKNGIKLD 

« Hide

References

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

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRT49274.
RefSeqNP_190447.1. NM_114737.4.
UniGeneAt.1379.
At.75040.

3D structure databases

ProteinModelPortalQ9M304.
SMRQ9M304. Positions 69-469.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING3702.AT3G48780.1-P.

Proteomic databases

PRIDEQ9M304.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT3G48780.1; AT3G48780.1; AT3G48780.
GeneID824039.
KEGGath:AT3G48780.

Organism-specific databases

TAIRAT3G48780.

Phylogenomic databases

HOGENOMHOG000206826.
InParanoidQ9M304.
KOK00654.
OMACADASEE.
PhylomeDBQ9M304.

Enzyme and pathway databases

BioCycARA:AT3G48780-MONOMER.
UniPathwayUPA00222.

Gene expression databases

GenevestigatorQ9M304.

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

PROQ9M304.

Entry information

Entry nameLCB2B_ARATH
AccessionPrimary (citable) accession number: Q9M304
Secondary accession number(s): Q0WMY9
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: October 1, 2000
Last modified: May 14, 2014
This is version 97 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