SLD2_ARATH
ID SLD2_ARATH Reviewed; 449 AA.
AC Q3EBF7;
DT 11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Delta(8)-fatty-acid desaturase 2;
DE EC=1.14.19.29 {ECO:0000269|PubMed:22023480};
DE AltName: Full=Delta(8)-sphingolipid desaturase 2;
DE AltName: Full=Sphingoid long-chain base desaturase 2;
DE Short=Sphingoid LCB desaturase 2;
DE AltName: Full=Sphingolipid 8-(E/Z)-desaturase 2;
GN Name=SLD2; OrderedLocusNames=At2g46210; ORFNames=T3F17.14;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=22023480; DOI=10.1111/j.1365-313x.2011.04829.x;
RA Chen M., Markham J.E., Cahoon E.B.;
RT "Sphingolipid Delta8 unsaturation is important for glucosylceramide
RT biosynthesis and low-temperature performance in Arabidopsis.";
RL Plant J. 69:769-781(2012).
CC -!- FUNCTION: Plays a major role as delta(8)-fatty-acid desaturase which
CC introduces a double bond at the 8-position in the long-chain base (LCB)
CC of ceramides with or without a hydroxy group at the 4-position. The
CC enzyme produces both the 8E and 8Z isomers (in a 4:1 ratio). This
CC structural modification contributes to the quantitative partitioning of
CC ceramides between the two major sphingolipid classes, glucosylceramides
CC and glycosylinositolphosphoryl ceramides. Sphingolipids are important
CC membrane components involved in environmental stress responses, such as
CC resistance to chilling, and act as cell signaling molecules.
CC {ECO:0000269|PubMed:22023480}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an N-acyl-(4R)-4-hydroxysphinganine + 2 Fe(II)-[cytochrome b5]
CC + 2 H(+) + O2 = a (4R,8E)-4-hydroxysphingenine ceramide + 2 Fe(III)-
CC [cytochrome b5] + 2 H2O; Xref=Rhea:RHEA:46268, Rhea:RHEA-COMP:10438,
CC Rhea:RHEA-COMP:10439, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:29033, ChEBI:CHEBI:29034,
CC ChEBI:CHEBI:31998, ChEBI:CHEBI:50934; EC=1.14.19.29;
CC Evidence={ECO:0000269|PubMed:22023480};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an N-acyl-(4R)-4-hydroxysphinganine + 2 Fe(II)-[cytochrome b5]
CC + 2 H(+) + O2 = (4R,8Z)-4-hydroxysphing-8-enine ceramide + 2 Fe(III)-
CC [cytochrome b5] + 2 H2O; Xref=Rhea:RHEA:46272, Rhea:RHEA-COMP:10438,
CC Rhea:RHEA-COMP:10439, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:29033, ChEBI:CHEBI:29034,
CC ChEBI:CHEBI:31998, ChEBI:CHEBI:85951; EC=1.14.19.29;
CC Evidence={ECO:0000269|PubMed:22023480};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875; Evidence={ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000305|PubMed:22023480}; Multi-pass membrane protein
CC {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Highly expressed in flowers and siliques. Expressed
CC at low levels in roots, leaves and stems.
CC {ECO:0000269|PubMed:22023480}.
CC -!- DOMAIN: The histidine box domains may contain the active site and/or be
CC involved in metal ion binding. {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions, but mutant plants show enhanced sensitivity to prolonged
CC low-temperature exposure. {ECO:0000269|PubMed:22023480}.
CC -!- SIMILARITY: Belongs to the fatty acid desaturase type 1 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AK228217; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AC005397; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002685; AEC10657.1; -; Genomic_DNA.
DR EMBL; AK228217; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; NP_182144.1; NM_130183.4.
DR AlphaFoldDB; Q3EBF7; -.
DR SMR; Q3EBF7; -.
DR STRING; 3702.AT2G46210.1; -.
DR PaxDb; Q3EBF7; -.
DR PRIDE; Q3EBF7; -.
DR ProteomicsDB; 228439; -.
DR EnsemblPlants; AT2G46210.1; AT2G46210.1; AT2G46210.
DR GeneID; 819228; -.
DR Gramene; AT2G46210.1; AT2G46210.1; AT2G46210.
DR KEGG; ath:AT2G46210; -.
DR Araport; AT2G46210; -.
DR TAIR; locus:2062928; AT2G46210.
DR eggNOG; KOG4232; Eukaryota.
DR HOGENOM; CLU_016265_2_0_1; -.
DR InParanoid; Q3EBF7; -.
DR OMA; DRWLVIS; -.
DR OrthoDB; 1060606at2759; -.
DR PhylomeDB; Q3EBF7; -.
DR BRENDA; 1.14.19.29; 399.
DR BRENDA; 1.14.19.4; 399.
DR PRO; PR:Q3EBF7; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q3EBF7; baseline and differential.
DR Genevisible; Q3EBF7; AT.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:UniProtKB.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016717; F:oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water; IBA:GO_Central.
DR GO; GO:0052631; F:sphingolipid delta-8 desaturase activity; IMP:UniProtKB.
DR GO; GO:0070417; P:cellular response to cold; IMP:UniProtKB.
DR GO; GO:0006629; P:lipid metabolic process; IBA:GO_Central.
DR GO; GO:0030148; P:sphingolipid biosynthetic process; IMP:UniProtKB.
DR Gene3D; 3.10.120.10; -; 1.
DR InterPro; IPR001199; Cyt_B5-like_heme/steroid-bd.
DR InterPro; IPR036400; Cyt_B5-like_heme/steroid_sf.
DR InterPro; IPR005804; FA_desaturase_dom.
DR InterPro; IPR012171; Fatty_acid_desaturase.
DR PANTHER; PTHR19353; PTHR19353; 1.
DR Pfam; PF00173; Cyt-b5; 1.
DR Pfam; PF00487; FA_desaturase; 1.
DR PIRSF; PIRSF015921; FA_sphinglp_des; 1.
DR SMART; SM01117; Cyt-b5; 1.
DR SUPFAM; SSF55856; SSF55856; 1.
DR PROSITE; PS50255; CYTOCHROME_B5_2; 1.
PE 1: Evidence at protein level;
KW Electron transport; Endoplasmic reticulum; Heme; Iron; Lipid metabolism;
KW Membrane; Metal-binding; Oxidoreductase; Reference proteome;
KW Sphingolipid metabolism; Transmembrane; Transmembrane helix; Transport.
FT CHAIN 1..449
FT /note="Delta(8)-fatty-acid desaturase 2"
FT /id="PRO_0000429374"
FT TRANSMEM 113..133
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 138..158
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 176..196
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 255..275
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 284..304
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 311..331
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 7..91
FT /note="Cytochrome b5 heme-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00279"
FT MOTIF 160..164
FT /note="Histidine box-1"
FT /evidence="ECO:0000305"
FT MOTIF 197..201
FT /note="Histidine box-2"
FT /evidence="ECO:0000305"
FT MOTIF 374..378
FT /note="Histidine box-3"
FT /evidence="ECO:0000305"
FT BINDING 42
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00279"
FT BINDING 65
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00279"
FT CONFLICT 372
FT /note="Q -> R (in Ref. 3; AK228217)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 449 AA; 51498 MW; 26C0338F460C10BD CRC64;
MADQTKKRYV TSEDLKKHNK PGDLWISIQG KVYDVSDWVK SHPGGEAAIL NLAGQDVTDA
FIAYHPGTAW HHLEKLHNGY HVRDHHVSDV SRDYRRLAAE FSKRGLFDKK GHVTLYTLTC
VGVMLAAVLY GVLACTSIWA HLISAVLLGL LWIQSAYVGH DSGHYTVTST KPCNKLIQLL
SGNCLTGISI AWWKWTHNAH HIACNSLDHD PDLQHIPIFA VSTKFFNSMT SRFYGRKLTF
DPLARFLISY QHWTFYPVMC VGRINLFIQT FLLLFSKRHV PDRALNIAGI LVFWTWFPLL
VSFLPNWQER FIFVFVSFAV TAIQHVQFCL NHFAADVYTG PPNGNDWFEK QTAGTLDISC
RSFMDWFFGG LQFQLEHHLF PRLPRCHLRT VSPVVKELCK KHNLPYRSLS WWEANVWTIR
TLKNAAIQAR DATNPVLKNL LWEAVNTHG
