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Q2R3K3

- LCB2A_ORYSJ

UniProt

Q2R3K3 - LCB2A_ORYSJ

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Protein

Long chain base biosynthesis protein 2a

Gene
Os11g0516000, LOC_Os11g31640, OsJ_34042
Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at transcript leveli

Functioni

Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1 constitutes the catalytic core By similarity.

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: UniProtKB-EC

GO - Biological processi

  1. photomorphogenesis Source: EnsemblPlants/Gramene
  2. pollen development Source: EnsemblPlants/Gramene
  3. regulation of programmed cell death Source: EnsemblPlants/Gramene
  4. sphingosine biosynthetic process Source: EnsemblPlants/Gramene
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Lipid metabolism, Sphingolipid metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

ReactomeiREACT_220105. Sphingolipid de novo biosynthesis.
UniPathwayiUPA00222.

Names & Taxonomyi

Protein namesi
Recommended name:
Long chain base biosynthesis protein 2a (EC:2.3.1.50)
Gene namesi
Ordered Locus Names:Os11g0516000, LOC_Os11g31640
ORF Names:OsJ_34042
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
ProteomesiUP000000763: Chromosome 11

Organism-specific databases

GrameneiQ2R3K3.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei4 – 2421Helical; Reviewed predictionAdd
BLAST

GO - Cellular componenti

  1. endoplasmic reticulum membrane Source: UniProtKB-SubCell
  2. integral component of membrane Source: UniProtKB-KW
  3. vacuole Source: EnsemblPlants/Gramene
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 488488Long chain base biosynthesis protein 2aPRO_0000419150Add
BLAST

Amino acid modifications

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

Interactioni

Subunit structurei

Heterodimer with LCB1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1 and LCB2 By similarity.

Structurei

3D structure databases

ProteinModelPortaliQ2R3K3.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
KOiK00654.
OMAiPEPGGCC.

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.

Q2R3K3-1 [UniParc]FASTAAdd to Basket

« Hide

MVRLPYTTAL TTLFSYGLLF AFGQLRDFFR KLIDWFKAKN VKGYAPICLG    50
LEDFYVRRLY LRIQDCFGRP IASAPDAWFD VVERYSNDSN KTLKRTSNTT 100
RCLNLGSYNY LGFAAADEYC TPLVIESLKK YSPSTCSVRV DGGTTKLHTE 150
LEELVARFVG KPAAILFGMG YVTNSAIIPC LVGKGGLIIS DSLNHNSIVN 200
GARGSGATVR VFQHNSPAHL EEVLREQIAG GQPRTHRPWK KIIVIVEGIY 250
SMEGELCKLP EIIAVCKKYK AYTYLDEAHS IGAVGQSGRG VCELLGVDPA 300
DVDIMMGTFT KSFGSCGGYI AASKEIIQHL KLSCPAHIYA TSMSPPAVQQ 350
VISAIKVILG EDGSNRGAQK LARIRENSNF FRSELKKMGF EVLGDNDSPV 400
MPIMLYNPAK IPAFSRECLR QKVAVVTVAF PATPLLLARA RICISASHTR 450
EDLIKALDVI SRVGDLVGIK YFPAEPPKIA EADHDKLE 488
Length:488
Mass (Da):53,690
Last modified:January 24, 2006 - v1
Checksum:iE4478AE71F6F8373
GO

Sequence cautioni

The sequence EEE52176.1 differs from that shown. Reason: Erroneous gene model prediction.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti289 – 2891R → W in AK069007. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
DP000010 Genomic DNA. Translation: ABA93932.1.
AP008217 Genomic DNA. Translation: BAF28335.1.
CM000148 Genomic DNA. Translation: EEE52176.1. Sequence problems.
AK069007 mRNA. No translation available.
RefSeqiNP_001067972.1. NM_001074504.1.
UniGeneiOs.7816.

Genome annotation databases

EnsemblPlantsiOS11T0516000-01; OS11T0516000-01; OS11G0516000.
GeneIDi4350591.
KEGGiosa:4350591.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
DP000010 Genomic DNA. Translation: ABA93932.1 .
AP008217 Genomic DNA. Translation: BAF28335.1 .
CM000148 Genomic DNA. Translation: EEE52176.1 . Sequence problems.
AK069007 mRNA. No translation available.
RefSeqi NP_001067972.1. NM_001074504.1.
UniGenei Os.7816.

3D structure databases

ProteinModelPortali Q2R3K3.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi OS11T0516000-01 ; OS11T0516000-01 ; OS11G0516000 .
GeneIDi 4350591.
KEGGi osa:4350591.

Organism-specific databases

Gramenei Q2R3K3.

Phylogenomic databases

eggNOGi COG0156.
KOi K00654.
OMAi PEPGGCC.

Enzyme and pathway databases

UniPathwayi UPA00222 .
Reactomei REACT_220105. Sphingolipid de novo biosynthesis.

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. "The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications."
    The rice chromosomes 11 and 12 sequencing consortia
    BMC Biol. 3:20-20(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  3. "The rice annotation project database (RAP-DB): 2008 update."
    The rice annotation project (RAP)
    Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  4. "The genomes of Oryza sativa: a history of duplications."
    Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.
    , Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.
    PLoS Biol. 3:266-281(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  5. "Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice."
    The rice full-length cDNA consortium
    Science 301:376-379(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Nipponbare.

Entry informationi

Entry nameiLCB2A_ORYSJ
AccessioniPrimary (citable) accession number: Q2R3K3
Secondary accession number(s): B9GAX0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: January 24, 2006
Last modified: September 3, 2014
This is version 71 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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