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Q5JK39

- LCB2D_ORYSJ

UniProt

Q5JK39 - LCB2D_ORYSJ

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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

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 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

Topology

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

GO - Cellular componenti

  1. endoplasmic reticulum Source: UniProtKB-KW
  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 – 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...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0156.
InParanoidiQ5JK39.
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

« Hide

        10         20         30         40         50
MVRLPYVTAL TTLFSYGLLF AFGQLRDFFR RILDAGKSSN LKGYAPICLG
60 70 80 90 100
LEDFYTRRLY LRIQDCFGRP IASAPDAWFD VVERYSNDSN KTLHRTTKTS
110 120 130 140 150
KCLNLGSYNY LGFAAADEYC TPRVIESLKK YSASTCSVRV DGGNTKLHVE
160 170 180 190 200
LEELVARFVG KPAAILFGMG YVTNSAIIPA LVGKGGLIIS DSLNHNSIVN
210 220 230 240 250
GARGSGATVR VFQHNNPAHL EEVLREQIAG GQPRTHRPWK KIIVIVEGIY
260 270 280 290 300
SMEGELCKLP EVIAVCKKYK AYTYLDEAHS IGAVGKTGRG VCELLGVDPA
310 320 330 340 350
DVDIMMGTFT KSFGSCGGYI AASKEIIDHL KHICPAHIYA TSMSPPAVQQ
360 370 380 390 400
VISAIKVILG EDGSNRGAKK LAQIRENSNF FRSELQKMGF EVLGDNDSPV
410 420 430 440 450
MPIMLYNPAK IPAFSRECLR QHVAVVTVAF PATPLLLARA RICISASHSR
460 470 480
EDLIKGLEVI SKVGDLVGIK YFPVEHEKTA SVEKLKKLQ
Length:489
Mass (Da):53,700
Last modified:February 15, 2005 - v1
Checksum:i9CCA90E8891B245B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.
InParanoidi Q5JK39.
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

« 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. "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: November 26, 2014
This is version 74 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