Q9M304 (LCB2B_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	489 AA.
Sequence status	Complete.
Protein existence	Evidence 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. Double mutant lcb2a/lcb2b was not viable due to pollen lethality. Ref.6
Sequence similarities	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.

Ontologies

Keywords
Biological process	Lipid metabolism Sphingolipid metabolism
Cellular component	Endoplasmic reticulum Membrane
Domain	Transmembrane Transmembrane helix
Ligand	Pyridoxal phosphate
Molecular function	Acyltransferase Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	photomorphogenesis Inferred from mutant phenotype Ref.6. Source: TAIR pollen development Inferred from mutant phenotype Ref.6. Source: TAIR sphingolipid biosynthetic process Inferred from mutant phenotype Ref.6. Source: TAIR
Cellular_component	endoplasmic reticulum membrane Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro serine C-palmitoyltransferase activity Inferred from genetic interaction Ref.6. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 489	489	Long chain base biosynthesis protein 2b		PRO_0000419146
Regions
	Transmembrane	2 – 22	21	Helical; Potential
Amino acid modifications
	Modified residue	311	1	N6-(pyridoxal phosphate)lysine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q9M304 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: BE059A00F5632105	FASTA	489	53,863
	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

References

	« Hide 'large scale' referencesShow '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. , 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.
+	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.
IPI	IPI00547826.
PIR	T49274.
RefSeq	NP_190447.1. NM_114737.4.
UniGene	At.1379. At.75040.
3D structure databases
ProteinModelPortal	Q9M304.
SMR	Q9M304. Positions 69-469.
ModBase	Search...
Protein-protein interaction databases
STRING	3702.AT3G48780.1-P.
Proteomic databases
PRIDE	Q9M304.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT3G48780.1; AT3G48780.1; AT3G48780.
GeneID	824039.
KEGG	ath:AT3G48780.
Organism-specific databases
TAIR	At3g48780.
Phylogenomic databases
HOGENOM	HOG000206826.
InParanoid	Q9M304.
KO	K00654.
OMA	ITAEHTK.
PhylomeDB	Q9M304.
ProtClustDB	PLN02483.
Enzyme and pathway databases
UniPathway	UPA00222.
Gene expression databases
Genevestigator	Q9M304.
Family and domain databases
Gene3D	3.40.640.10. 1 hit. 3.90.1150.10. 1 hit.
InterPro	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]
Pfam	PF00155. Aminotran_1_2. 1 hit. [Graphical view]
SUPFAM	SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
PROSITE	PS00599. AA_TRANSFER_CLASS_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

LCB2B_ARATH

Accession

Primary (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 1, 2013
This is version 91 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program