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Q5JK39

- LCB2D_ORYSJ

UniProt

Q5JK39 - LCB2D_ORYSJ

Protein

Long chain base biosynthesis protein 2d

Gene

Os01g0928800

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 72 (01 Oct 2014)
      Sequence version 1 (15 Feb 2005)
      Previous versions | rss
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    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

    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. biosynthetic process Source: InterPro
    2. sphingolipid metabolic process Source: UniProtKB-UniPathway

    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 2d (EC:2.3.1.50)
    Gene namesi
    Ordered Locus Names:Os01g0928800, LOC_Os01g70380
    ORF Names:OsJ_04635, OSJNBa0052O12.15
    OrganismiOryza sativa subsp. japonica (Rice)
    Taxonomic identifieri39947 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
    ProteomesiUP000000763: Chromosome 1

    Organism-specific databases

    GrameneiQ5JK39.

    Subcellular locationi

    GO - Cellular componenti

    1. endoplasmic reticulum membrane Source: UniProtKB-SubCell
    2. integral component of membrane Source: UniProtKB-KW

    Keywords - Cellular componenti

    Endoplasmic reticulum, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 489489Long chain base biosynthesis protein 2dPRO_0000419153Add
    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

    ProteinModelPortaliQ5JK39.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei4 – 2421HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG0156.
    KOiK00654.
    OMAiICLGHED.

    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.

    Q5JK39-1 [UniParc]FASTAAdd to Basket

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    MVRLPYVTAL TTLFSYGLLF AFGQLRDFFR RILDAGKSSN LKGYAPICLG    50
    LEDFYTRRLY LRIQDCFGRP IASAPDAWFD VVERYSNDSN KTLHRTTKTS 100
    KCLNLGSYNY LGFAAADEYC TPRVIESLKK YSASTCSVRV DGGNTKLHVE 150
    LEELVARFVG KPAAILFGMG YVTNSAIIPA LVGKGGLIIS DSLNHNSIVN 200
    GARGSGATVR VFQHNNPAHL EEVLREQIAG GQPRTHRPWK KIIVIVEGIY 250
    SMEGELCKLP EVIAVCKKYK AYTYLDEAHS IGAVGKTGRG VCELLGVDPA 300
    DVDIMMGTFT KSFGSCGGYI AASKEIIDHL KHICPAHIYA TSMSPPAVQQ 350
    VISAIKVILG EDGSNRGAKK LAQIRENSNF FRSELQKMGF EVLGDNDSPV 400
    MPIMLYNPAK IPAFSRECLR QHVAVVTVAF PATPLLLARA RICISASHSR 450
    EDLIKGLEVI SKVGDLVGIK YFPVEHEKTA SVEKLKKLQ 489
    Length:489
    Mass (Da):53,700
    Last modified:February 15, 2005 - v1
    Checksum:i9CCA90E8891B245B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP004330 Genomic DNA. Translation: BAD88168.1.
    AP008207 Genomic DNA. Translation: BAF07193.1.
    CM000138 Genomic DNA. Translation: EEE55940.1.
    AK120617 mRNA. Translation: BAH00095.1.
    RefSeqiNP_001045279.1. NM_001051814.1.
    UniGeneiOs.22885.

    Genome annotation databases

    EnsemblPlantsiOS01T0928800-01; OS01T0928800-01; OS01G0928800.
    GeneIDi4326966.
    KEGGiosa:4326966.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP004330 Genomic DNA. Translation: BAD88168.1 .
    AP008207 Genomic DNA. Translation: BAF07193.1 .
    CM000138 Genomic DNA. Translation: EEE55940.1 .
    AK120617 mRNA. Translation: BAH00095.1 .
    RefSeqi NP_001045279.1. NM_001051814.1.
    UniGenei Os.22885.

    3D structure databases

    ProteinModelPortali Q5JK39.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi OS01T0928800-01 ; OS01T0928800-01 ; OS01G0928800 .
    GeneIDi 4326966.
    KEGGi osa:4326966.

    Organism-specific databases

    Gramenei Q5JK39.

    Phylogenomic databases

    eggNOGi COG0156.
    KOi K00654.
    OMAi ICLGHED.

    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

    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. "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 nameiLCB2D_ORYSJ
    AccessioniPrimary (citable) accession number: Q5JK39
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 3, 2012
    Last sequence update: February 15, 2005
    Last modified: October 1, 2014
    This is version 72 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