PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Neem_10442_f_1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family LSD
Protein Properties Length: 152aa    MW: 16295.9 Da    PI: 8.3394
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_10442_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD137.73.3e-122145125
         zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                    C gCrtlL+ + GA+sVRC++C+tV
  Neem_10442_f_1 21 CRGCRTLLMHTHGATSVRCSCCHTV 45
                    9***********************9 PP

2zf-LSD147.43.1e-156286125
         zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                    Cg+Crt+L+YP+GApsV+Ca+C+ V
  Neem_10442_f_1 62 CGHCRTTLMYPYGAPSVKCAVCHYV 86
                    **********************987 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR010537.6E-141847IPR005735Zinc finger, LSD1-type
Gene3DG3DSA:3.90.10.103.6E-42087No hitNo description
PfamPF069431.8E-102145IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010531.5E-125989IPR005735Zinc finger, LSD1-type
PfamPF069434.0E-146286IPR005735Zinc finger, LSD1-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000303Biological Processresponse to superoxide
GO:0001666Biological Processresponse to hypoxia
GO:0002240Biological Processresponse to molecule of oomycetes origin
GO:0009626Biological Processplant-type hypersensitive response
GO:0009862Biological Processsystemic acquired resistance, salicylic acid mediated signaling pathway
GO:0010104Biological Processregulation of ethylene-activated signaling pathway
GO:0010310Biological Processregulation of hydrogen peroxide metabolic process
GO:0010602Biological Processregulation of 1-aminocyclopropane-1-carboxylate metabolic process
GO:0010618Biological Processaerenchyma formation
GO:0043069Biological Processnegative regulation of programmed cell death
Sequence ? help Back to Top
Protein Sequence    Length: 152 aa     Download sequence    Send to blast
MFDHQSLYNG SAGMEMAQLI CRGCRTLLMH THGATSVRCS CCHTVNPVNL SPAPNQLAHI  60
NCGHCRTTLM YPYGAPSVKC AVCHYVTNVG MANVRVPLPA NRPMSTPGTL PSTSMPMPHS  120
QTQTVVVENP MSVDESGKLV SNVVVGVTTE KK
Functional Description ? help Back to Top
Source Description
UniProtNegative regulator of reactive oxygen-induced cell death, cold stress-induced cell death, pathogen-induced hypersensitive response (HR), basal disease resistance. May be involved in the induction of the copper/zinc superoxide dismutase CSD1 and CSD2 that detoxify accumulating superoxide before the reactive oxygen species (ROS) can trigger a cell death cascade. LSD1 and LOL1 have antagonistic effects on CSD1 and CSD2 accumulation to regulate oxidative stress-induced cell death. Antagonizes the function of BZIP10, a positive regulator of cell death, by interacting in the cytoplasm and preventing its nuclear localization. Controls lysigenous aerenchyma in hypocotyls under root hypoxia. Required for leaf acclimation in response to excess excitation energy. {ECO:0000269|PubMed:10550898, ECO:0000269|PubMed:11595797, ECO:0000269|PubMed:11844114, ECO:0000269|PubMed:12732715, ECO:0000269|PubMed:15347794, ECO:0000269|PubMed:16957775, ECO:0000269|PubMed:18055613, ECO:0000269|PubMed:18790826, ECO:0000269|PubMed:20456049, ECO:0000269|PubMed:21097903}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By methyl viologen. {ECO:0000269|PubMed:20456049}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012075549.17e-78protein LSD1 isoform X1
SwissprotP940773e-53LSD1_ARATH; Protein LSD1
TrEMBLA0A067KSR62e-76A0A067KSR6_JATCU; Uncharacterized protein
STRINGevm.model.supercontig_832.23e-74(Carica papaya)
STRINGPOPTR_0001s43300.14e-74(Populus trichocarpa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM53452650
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G20380.71e-55LSD family protein
Publications ? help Back to Top
  1. Spedaletti V, et al.
    Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana.
    Biochemistry, 2008. 47(17): p. 4936-47
    [PMID:18393445]
  2. Szechyńska-Hebda M,Czarnocka W,Hebda M,Bernacki MJ,Karpiński S
    PAD4, LSD1 and EDS1 regulate drought tolerance, plant biomass production, and cell wall properties.
    Plant Cell Rep., 2016. 35(3): p. 527-39
    [PMID:26754794]
  3. Czarnocka W, et al.
    The dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator.
    Plant Cell Environ., 2017. 40(11): p. 2644-2662
    [PMID:28555890]
  4. Bernacki MJ, et al.
    LSD1-, EDS1- and PAD4-dependent conditional correlation among salicylic acid, hydrogen peroxide, water use efficiency and seed yield in Arabidopsis thaliana.
    Physiol Plant, 2019. 165(2): p. 369-382
    [PMID:30461017]