PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Vang0045ss00360.1

Organism

Vigna angularis

Taxonomic ID

3914

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna

Family

LSD

Protein Properties

Length: 238aa MW: 25704.8 Da PI: 8.578

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Vang0045ss00360.1	genome	SNU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	42.4	1.2e-13	37	61	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr lL YPrGA++V+CalC+t+ Vang0045ss00360.1 37 CNGCRSLLLYPRGATNVCCALCNTI 61 ***********************97 PP
2	zf-LSD1	49.1	9.4e-16	76	100	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggCrtlL+Y+rGA+sVRC++C+tV Vang0045ss00360.1 76 CGGCRTLLMYTRGATSVRCSCCHTV 100 ************************9 PP
3	zf-LSD1	44.8	2.1e-14	174	198	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Crt L+YP+GApsV+Ca+C+ V Vang0045ss00360.1 174 CGNCRTALMYPYGAPSVKCAICHYV 198 **********************987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	1.4E-12	34	64	IPR005735	Zinc finger, LSD1-type
Gene3D	G3DSA:3.90.10.10	6.2E-4	34	98	No hit	No description
Pfam	PF06943	1.3E-11	37	61	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.8E-17	73	103	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	4.0E-13	76	100	IPR005735	Zinc finger, LSD1-type
Gene3D	G3DSA:3.90.10.10	6.2E-4	153	205	No hit	No description
TIGRFAMs	TIGR01053	3.7E-12	171	199	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.8E-13	174	198	IPR005735	Zinc finger, LSD1-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000303	Biological Process	response to superoxide
GO:0001666	Biological Process	response to hypoxia
GO:0002240	Biological Process	response to molecule of oomycetes origin
GO:0009626	Biological Process	plant-type hypersensitive response
GO:0009862	Biological Process	systemic acquired resistance, salicylic acid mediated signaling pathway
GO:0010104	Biological Process	regulation of ethylene-activated signaling pathway
GO:0010310	Biological Process	regulation of hydrogen peroxide metabolic process
GO:0010602	Biological Process	regulation of 1-aminocyclopropane-1-carboxylate metabolic process
GO:0010618	Biological Process	aerenchyma formation
GO:0043069	Biological Process	negative regulation of programmed cell death

Sequence ? help Back to Top
Protein Sequence Length: 238 aa Download sequence Send to blast
MRKYCHSGSG FLFYLQNKSV GILVELSVTP MQSQLVCNGC RSLLLYPRGA TNVCCALCNT 60 ITSVPPPGME MSQLYCGGCR TLLMYTRGAT SVRCSCCHTV NLVPVNGDLM KRFTVGLEGK 120 EYWWFLGKNG YGDFPWNLSI YGTGRFVAAT SFTEIAAVGW GLAKATNQVA HVHCGNCRTA 180 LMYPYGAPSV KCAICHYVTN SMPQSQSQTV VVENPMSVDS SGKLVSNVVV GVTTDKK*

Functional Description ? help Back to Top
Source	Description
UniProt	Negative 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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Vang0045ss00360.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By methyl viologen. {ECO:0000269\|PubMed:20456049}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT096707	3e-95	BT096707.1 Soybean clone JCVI-FLGm-21G1 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025984159.1	3e-76	uncharacterized protein LOC100776394 isoform X2
Refseq	XP_028233007.1	3e-76	protein LSD1-like isoform X2
Swissprot	P94077	2e-53	LSD1_ARATH; Protein LSD1
TrEMBL	A0A151TKM2	2e-86	A0A151TKM2_CAJCA; Uncharacterized protein
STRING	Lus10008066	1e-67	(Linum usitatissimum)
STRING	XP_004293683.1	1e-66	(Fragaria vesca)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4027	33	61

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.8	6e-58	LSD family protein

Publications ? help Back to Top
Spedaletti V, et al. Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana. Biochemistry, 2008. 47(17): p. 4936-47 [PMID:18393445] 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] 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] 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]