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Protein

Long chain base biosynthesis protein 2b

Gene

Os01g0928600

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 2b (EC:2.3.1.50)
Gene namesi
Ordered Locus Names:Os01g0928600, LOC_Os01g70360
ORF Names:OsJ_04633, OSJNBa0052O12.11
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
ProteomesiUP000000763: Chromosome 1

Organism-specific databases

GrameneiQ8RYL1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei5 – 2521HelicalSequence 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 – 499499Long chain base biosynthesis protein 2bPRO_0000419151Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei322 – 3221N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

PRIDEiQ8RYL1.

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

ProteinModelPortaliQ8RYL1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
InParanoidiQ8RYL1.
OMAiNPFFRVH.

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.

Q8RYL1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MVIKVPYVTA ATTLFSFGLI FGFGHLRDSF RALLRLLFSS AAAADSPAGC
60 70 80 90 100
NSKGYAPICV GKEDFYIRRF FRRVQDCFGR PIASKPDAWF DVVERYSTDS
110 120 130 140 150
NKTLHCTTKT SKCLNLASFN YLGFAAADEY CTPRVIESLK KYSASTCSSR
160 170 180 190 200
VDGGNTQLHI ELEELVARFV RKPSAILLAM GYATNSAIIP ALIGKGGLII
210 220 230 240 250
SDSLNHNSIV SGARASGATI RVFEHNNPAH LEKLLREQIS GGQPRTHRAW
260 270 280 290 300
KKILVIVEGI YSMEGELCKL PEIISVCKKY KVYTYMDEAH SIGAVGKTGR
310 320 330 340 350
GVCELLGVDP ADVDIMMGTL SKSFGSSGGY IAASKEIIQH LKLTCPSHIY
360 370 380 390 400
GTSMSPPAVQ QVISAMKVIL GEDGTDRGAK KIAQIRDNSN FFRSELQKMG
410 420 430 440 450
FEVLGDNDSP VMPFMVYNPA KMPAFSRECL KQNVAVVPVG FPATPLLLGR
460 470 480 490
IRICISASHS REDLIKGLEV ISNVGDLVGI KYLPVEQEET TSVEKPKKL
Length:499
Mass (Da):54,484
Last modified:June 1, 2002 - v1
Checksum:iDE09CFF7BA824CCF
GO

Sequence cautioni

The sequence BAF07191.2 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP004330 Genomic DNA. Translation: BAB90751.1.
AP008207 Genomic DNA. Translation: BAF07191.2. Sequence problems.
CM000138 Genomic DNA. Translation: EAZ14709.1.
AK241034 mRNA. Translation: BAH00934.1.
RefSeqiNP_001045277.2. NM_001051812.2.
UniGeneiOs.42735.

Genome annotation databases

EnsemblPlantsiOS01T0928600-01; OS01T0928600-01; OS01G0928600.
GeneIDi4326964.
KEGGiosa:4326964.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP004330 Genomic DNA. Translation: BAB90751.1.
AP008207 Genomic DNA. Translation: BAF07191.2. Sequence problems.
CM000138 Genomic DNA. Translation: EAZ14709.1.
AK241034 mRNA. Translation: BAH00934.1.
RefSeqiNP_001045277.2. NM_001051812.2.
UniGeneiOs.42735.

3D structure databases

ProteinModelPortaliQ8RYL1.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ8RYL1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiOS01T0928600-01; OS01T0928600-01; OS01G0928600.
GeneIDi4326964.
KEGGiosa:4326964.

Organism-specific databases

GrameneiQ8RYL1.

Phylogenomic databases

eggNOGiCOG0156.
InParanoidiQ8RYL1.
OMAiNPFFRVH.

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 genome sequence and structure of rice chromosome 1."
    Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y., Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H., Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.
    , Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M., Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T., Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S., Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H., Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y., Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S., Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y., Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S., Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H., Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.
    Nature 420:312-316(2002) [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. "Oryza sativa full length cDNA."
    The rice full-length cDNA consortium
    Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Nipponbare.

Entry informationi

Entry nameiLCB2B_ORYSJ
AccessioniPrimary (citable) accession number: Q8RYL1
Secondary accession number(s): Q0JGD7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: June 1, 2002
Last modified: January 7, 2015
This is version 85 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.