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Protein

Long chain base biosynthesis protein 2a

Gene

Os11g0516000

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: 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).By similarity

Catalytic activityi

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

Cofactori

Pathwayi

GO - Molecular functioni

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

GO - Biological processi

  1. biosynthetic process Source: InterPro
  2. sphingolipid metabolic process Source: UniProtKB-UniPathway
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 – 2421HelicalSequence AnalysisAdd
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

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)lysineBy similarity

Interactioni

Subunit structurei

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

Structurei

3D structure databases

ProteinModelPortaliQ2R3K3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
InParanoidiQ2R3K3.
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

        10         20         30         40         50
MVRLPYTTAL TTLFSYGLLF AFGQLRDFFR KLIDWFKAKN VKGYAPICLG
60 70 80 90 100
LEDFYVRRLY LRIQDCFGRP IASAPDAWFD VVERYSNDSN KTLKRTSNTT
110 120 130 140 150
RCLNLGSYNY LGFAAADEYC TPLVIESLKK YSPSTCSVRV DGGTTKLHTE
160 170 180 190 200
LEELVARFVG KPAAILFGMG YVTNSAIIPC LVGKGGLIIS DSLNHNSIVN
210 220 230 240 250
GARGSGATVR VFQHNSPAHL EEVLREQIAG GQPRTHRPWK KIIVIVEGIY
260 270 280 290 300
SMEGELCKLP EIIAVCKKYK AYTYLDEAHS IGAVGQSGRG VCELLGVDPA
310 320 330 340 350
DVDIMMGTFT KSFGSCGGYI AASKEIIQHL KLSCPAHIYA TSMSPPAVQQ
360 370 380 390 400
VISAIKVILG EDGSNRGAQK LARIRENSNF FRSELKKMGF EVLGDNDSPV
410 420 430 440 450
MPIMLYNPAK IPAFSRECLR QKVAVVTVAF PATPLLLARA RICISASHTR
460 470 480
EDLIKALDVI SRVGDLVGIK YFPAEPPKIA EADHDKLE
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. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti289 – 2891R → W in AK069007. (PubMed:12869764)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliQ2R3K3.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

GrameneiQ2R3K3.

Phylogenomic databases

eggNOGiCOG0156.
InParanoidiQ2R3K3.
KOiK00654.
OMAiPEPGGCC.

Enzyme and pathway databases

UniPathwayiUPA00222.
ReactomeiREACT_220105. Sphingolipid de novo biosynthesis.

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]
ProtoNetiSearch...

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: January 7, 2015
This is version 75 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.