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Q5JK39 (LCB2D_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 70. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Long chain base biosynthesis protein 2d

EC=2.3.1.50
Gene names
Ordered Locus Names:Os01g0928800, LOC_Os01g70380
ORF Names:OsJ_04635, OSJNBa0052O12.15
OrganismOryza sativa subsp. japonica (Rice) [Reference proteome]
Taxonomic identifier39947 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza

Protein attributes

Sequence length489 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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

Catalytic activity

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

Cofactor

Pyridoxal phosphate By similarity.

Pathway

Lipid metabolism; sphingolipid metabolism.

Subunit structure

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

Subcellular location

Endoplasmic reticulum membrane; Single-pass membrane protein By similarity.

Sequence similarities

Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 489489Long chain base biosynthesis protein 2d
PRO_0000419153

Regions

Transmembrane4 – 2421Helical; Potential

Amino acid modifications

Modified residue3111N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q5JK39 [UniParc].

Last modified February 15, 2005. Version 1.
Checksum: 9CCA90E8891B245B

FASTA48953,700
        10         20         30         40         50         60 
MVRLPYVTAL TTLFSYGLLF AFGQLRDFFR RILDAGKSSN LKGYAPICLG LEDFYTRRLY 

        70         80         90        100        110        120 
LRIQDCFGRP IASAPDAWFD VVERYSNDSN KTLHRTTKTS KCLNLGSYNY LGFAAADEYC 

       130        140        150        160        170        180 
TPRVIESLKK YSASTCSVRV DGGNTKLHVE LEELVARFVG KPAAILFGMG YVTNSAIIPA 

       190        200        210        220        230        240 
LVGKGGLIIS DSLNHNSIVN GARGSGATVR VFQHNNPAHL EEVLREQIAG GQPRTHRPWK 

       250        260        270        280        290        300 
KIIVIVEGIY SMEGELCKLP EVIAVCKKYK AYTYLDEAHS IGAVGKTGRG VCELLGVDPA 

       310        320        330        340        350        360 
DVDIMMGTFT KSFGSCGGYI AASKEIIDHL KHICPAHIYA TSMSPPAVQQ VISAIKVILG 

       370        380        390        400        410        420 
EDGSNRGAKK LAQIRENSNF FRSELQKMGF EVLGDNDSPV MPIMLYNPAK IPAFSRECLR 

       430        440        450        460        470        480 
QHVAVVTVAF PATPLLLARA RICISASHSR EDLIKGLEVI SKVGDLVGIK YFPVEHEKTA 


SVEKLKKLQ 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The map-based sequence of the rice genome."
International rice genome sequencing project (IRGSP)
Nature 436:793-800(2005) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AP004330 Genomic DNA. Translation: BAD88168.1.
AP008207 Genomic DNA. Translation: BAF07193.1.
CM000138 Genomic DNA. Translation: EEE55940.1.
AK120617 mRNA. Translation: BAH00095.1.
RefSeqNP_001045279.1. NM_001051814.1.
UniGeneOs.22885.

3D structure databases

ProteinModelPortalQ5JK39.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsOS01T0928800-01; OS01T0928800-01; OS01G0928800.
GeneID4326966.
KEGGosa:4326966.

Organism-specific databases

GrameneQ5JK39.

Phylogenomic databases

eggNOGCOG0156.
KOK00654.
OMAICLGHED.

Enzyme and pathway databases

UniPathwayUPA00222.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProIPR001917. 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]
PfamPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMSSF53383. SSF53383. 1 hit.
PROSITEPS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameLCB2D_ORYSJ
AccessionPrimary (citable) accession number: Q5JK39
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2012
Last sequence update: February 15, 2005
Last modified: May 14, 2014
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Oryza sativa (rice)

Index of Oryza sativa entries and their corresponding gene designations

PATHWAY comments

Index of metabolic and biosynthesis pathways