SLD1_ARATH
ID SLD1_ARATH Reviewed; 449 AA.
AC Q9ZRP7; Q8LB96;
DT 11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 161.
DE RecName: Full=Delta(8)-fatty-acid desaturase 1;
DE EC=1.14.19.29 {ECO:0000269|PubMed:22023480, ECO:0000269|PubMed:9786850};
DE AltName: Full=Delta(8)-sphingolipid desaturase 1;
DE AltName: Full=Sphingoid long-chain base desaturase 1;
DE Short=Sphingoid LCB desaturase 1;
DE AltName: Full=Sphingolipid 8-(E/Z)-desaturase 1;
GN Name=SLD1; OrderedLocusNames=At3g61580; ORFNames=F2A19.180;
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 [MRNA], FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=cv. Columbia;
RX PubMed=9786850; DOI=10.1074/jbc.273.44.28590;
RA Sperling P., Zaehringer U., Heinz E.;
RT "A sphingolipid desaturase from higher plants. Identification of a new
RT cytochrome b5 fusion protein.";
RL J. Biol. Chem. 273:28590-28596(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
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, ECO:0000269|PubMed:9786850}.
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, ECO:0000269|PubMed:9786850};
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, ECO:0000269|PubMed:9786850};
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. Expressed in roots,
CC leaves, stems and siliques. {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 have strongly reduced levels of
CC unsaturated LCB sphingolipids in all organs and show enhanced
CC sensitivity to prolonged low-temperature exposure.
CC {ECO:0000269|PubMed:22023480}.
CC -!- SIMILARITY: Belongs to the fatty acid desaturase type 1 family.
CC {ECO:0000305}.
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DR EMBL; AJ224161; CAA11858.1; -; mRNA.
DR EMBL; AL132962; CAB71088.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE80226.1; -; Genomic_DNA.
DR EMBL; AF428420; AAL16189.1; -; mRNA.
DR EMBL; BT000442; AAN17419.1; -; mRNA.
DR EMBL; BT003379; AAO30042.1; -; mRNA.
DR EMBL; AY087345; AAM64895.1; -; mRNA.
DR PIR; T47950; T47950.
DR RefSeq; NP_191717.1; NM_116023.2.
DR AlphaFoldDB; Q9ZRP7; -.
DR SMR; Q9ZRP7; -.
DR BioGRID; 10645; 1.
DR IntAct; Q9ZRP7; 1.
DR STRING; 3702.AT3G61580.1; -.
DR PaxDb; Q9ZRP7; -.
DR PRIDE; Q9ZRP7; -.
DR ProteomicsDB; 234493; -.
DR EnsemblPlants; AT3G61580.1; AT3G61580.1; AT3G61580.
DR GeneID; 825331; -.
DR Gramene; AT3G61580.1; AT3G61580.1; AT3G61580.
DR KEGG; ath:AT3G61580; -.
DR Araport; AT3G61580; -.
DR TAIR; locus:2082792; AT3G61580.
DR eggNOG; KOG4232; Eukaryota.
DR HOGENOM; CLU_016265_2_0_1; -.
DR InParanoid; Q9ZRP7; -.
DR OMA; TIDISCR; -.
DR OrthoDB; 1060606at2759; -.
DR PhylomeDB; Q9ZRP7; -.
DR BioCyc; ARA:AT3G61580-MON; -.
DR BioCyc; MetaCyc:AT3G61580-MON; -.
DR BRENDA; 1.14.19.29; 399.
DR BRENDA; 1.14.19.4; 399.
DR PRO; PR:Q9ZRP7; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9ZRP7; baseline and differential.
DR Genevisible; Q9ZRP7; 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; IDA:TAIR.
DR GO; GO:0070417; P:cellular response to cold; IMP:UniProtKB.
DR GO; GO:0006629; P:lipid metabolic process; IDA:TAIR.
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 1"
FT /id="PRO_0000429373"
FT TRANSMEM 113..133
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 138..158
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 173..195
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 127
FT /note="G -> R (in Ref. 5; AAM64895)"
FT /evidence="ECO:0000305"
FT CONFLICT 317
FT /note="S -> G (in Ref. 5; AAM64895)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 449 AA; 51675 MW; 145048F9F1D35964 CRC64;
MAEETEKKYI TNEDLKKHNK SGDLWIAIQG KVYNVSDWIK THPGGDTVIL NLVGQDVTDA
FIAFHPGTAW HHLDHLFTGY HIRDFQVSEV SRDYRRMAAE FRKLGLFENK GHVTLYTLAF
VAAMFLGVLY GVLACTSVFA HQIAAALLGL LWIQSAYIGH DSGHYVIMSN KSYNRFAQLL
SGNCLTGISI AWWKWTHNAH HLACNSLDYD PDLQHIPVFA VSTKFFSSLT SRFYDRKLTF
DPVARFLVSY QHFTYYPVMC FGRINLFIQT FLLLFSKREV PDRALNFAGI LVFWTWFPLL
VSCLPNWPER FFFVFTSFTV TALQHIQFTL NHFAADVYVG PPTGSDWFEK QAAGTIDISC
RSYMDWFFGG LQFQLEHHLF PRLPRCHLRK VSPVVQELCK KHNLPYRSMS WFEANVLTIN
TLKTAAYQAR DVANPVVKNL VWEALNTHG
