PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria

Family

bHLH

Protein Properties

Length: 1303aa MW: 144520 Da PI: 5.5669

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
mrna00901.1-v1.0-hybrid	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	11.9	0.00041	424	458	16	55
HHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 16 iNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 + +++ L++++ + +K + a++L +A++YIk Lq mrna00901.1-v1.0-hybrid 424 VADKITALQQIVSPF-----GKTDTASVLYEAIQYIKFLQ 458 568899999999998.....8******************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	10.074	408	457	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	4.32E-8	423	471	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.7E-7	424	465	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	0.00639	426	462	No hit	No description
SuperFamily	SSF52540	1.36E-41	711	897	IPR027417	P-loop containing nucleoside triphosphate hydrolase
SMART	SM00487	5.1E-32	719	924	IPR014001	Helicase superfamily 1/2, ATP-binding domain
Gene3D	G3DSA:3.40.50.300	1.0E-22	723	908	IPR027417	P-loop containing nucleoside triphosphate hydrolase
PROSITE profile	PS51192	18.922	736	914	IPR014001	Helicase superfamily 1/2, ATP-binding domain
Pfam	PF00176	4.7E-49	743	1058	IPR000330	SNF2-related, N-terminal domain
CDD	cd00046	6.02E-18	744	896	No hit	No description
SuperFamily	SSF52540	1.92E-60	855	898	IPR027417	P-loop containing nucleoside triphosphate hydrolase
SuperFamily	SSF52540	1.36E-41	927	978	IPR027417	P-loop containing nucleoside triphosphate hydrolase
SuperFamily	SSF52540	1.92E-60	935	941	IPR027417	P-loop containing nucleoside triphosphate hydrolase
SuperFamily	SSF52540	1.92E-60	1118	1282	IPR027417	P-loop containing nucleoside triphosphate hydrolase
Gene3D	G3DSA:3.40.50.300	2.1E-21	1126	1277	IPR027417	P-loop containing nucleoside triphosphate hydrolase
CDD	cd00079	1.31E-25	1126	1248	No hit	No description
Pfam	PF00271	2.8E-18	1128	1240	IPR001650	Helicase, C-terminal
PROSITE profile	PS51194	16.041	1131	1293	IPR001650	Helicase, C-terminal
SMART	SM00490	5.7E-20	1157	1240	IPR001650	Helicase, C-terminal

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006974	Biological Process	cellular response to DNA damage stimulus
GO:0071494	Biological Process	cellular response to UV-C
GO:0005524	Molecular Function	ATP binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009005	anatomy	root
PO:0007134	developmental stage	sporophyte vegetative stage

Sequence ? help Back to Top
Protein Sequence Length: 1303 aa Download sequence Send to blast
MAADQCRLDS TVNCVVISSS TQPNWWDHDH LHAAAAAAGA GSHLSASSWP WQRQQQQQQQ 60 QKPNPNSNSS CDEDVSISST SFTNASNHSS LSVDSSRRLV DQRSASSNDD LNNIGEQVSD 120 NQIWSHVLLS AGNNGLNGSM THDVGENFLD ALSSKNLTNT AMYDPACDYL KKLDNASSNW 180 EFTNSSTTAA TMHASNLNNF ERQININGSF SNENLSNLVS TWSIAPPEPQ LVSSPFFNNL 240 PHQVSCYGAH NNLMKVESAA QLAGANIHGR PFSSENGSNI DYQIGLNNAM AADNNYYGSG 300 NGLVMPDSYS SSNSARSFTD VISFNSRLGK PLIDHVHHAQ KPSNFKSSIN LSDNTCKKQG 360 LQTSSPVKMS GRGQGTANES AGKKKRTEDS STSSETVLKK PKQETSAANS SSSSVKMQAP 420 KVKVADKITA LQQIVSPFGK TDTASVLYEA IQYIKFLQDQ IHVQLSSSPY LKTNTHKQDS 480 WGKLDQIRGD HQVKMDLKSR GLCLVPTSCT PQLYSNSQSP ISDVMKRSLD DYEISDDEWE 540 EDHASSFKPS RVLNNKPPPR APPPPAIESF AYKRGRASSA DDADFVVDIS DGSDDDCVEI 600 KDDDLEDDDV EEEVVRSRPV TRGRRFVVED EDSDGDWAEL ESSSEEEEEE EAEAVGDDDV 660 VGRALQKCAK ISADLKRELH GSSAAATASD RYAEVDASSV RIVTQDDINE ACRSDQSDFL 720 PVLKPYQLVG VNFLLLLYRK GIGGAILADE MGLGKTIQAV TYLMLLKHLH KDPGPHLIVC 780 PASVLENWER ELKKWCPSFS VLQYHGAARS AYSRELTSLA KAGMPPPFNV ILVCYSLFER 840 HSAQQKDDRK ILKRWRWSCV LMDEAHALKD KNSYRWKNLM SVARSANQRL MLTGTPLQND 900 LHASFIVLVT PLSLGLDTLS RTLSSHLLFL SELWSMLEFI MPDLFTTEDV DLKKLLSTAD 960 TDLISRMKSI LGPFILRRLK SDVMQQLVPK IQRVEYVIME KEQNDAYKEA IEEYRAASRA 1020 RIAKTSQANT NSIIGVIPRR QISNYFVQFR KIANHPLLVR RIYSDEDVVR FARKLHPMGA 1080 FGFECTLDRV IEEMKSFNDF SIHRLLLSYD ITDKKGCLPD EDVMLSAKSQ ALAELLPILK 1140 QAGHRVLIFS QWTSMLDILE WALDVIGVTY RRLDGSTQVT ERQTIVDTFN NDTSIFACLL 1200 STRAGGQGLN LTGADTVVIH DMDFNPQIDR QAEDRCHRIG QTKPVTIYRL VTKGTVDENV 1260 YEIAKRKLVL DAAVLESGLE MENEGAASEK TMGEILSKLL LG*

Sequence ? help Back to Top

Protein Sequence Length: 1303 aa Download sequence Send to blast

MAADQCRLDS TVNCVVISSS TQPNWWDHDH LHAAAAAAGA GSHLSASSWP WQRQQQQQQQ  60
QKPNPNSNSS CDEDVSISST SFTNASNHSS LSVDSSRRLV DQRSASSNDD LNNIGEQVSD  120
NQIWSHVLLS AGNNGLNGSM THDVGENFLD ALSSKNLTNT AMYDPACDYL KKLDNASSNW  180
EFTNSSTTAA TMHASNLNNF ERQININGSF SNENLSNLVS TWSIAPPEPQ LVSSPFFNNL  240
PHQVSCYGAH NNLMKVESAA QLAGANIHGR PFSSENGSNI DYQIGLNNAM AADNNYYGSG  300
NGLVMPDSYS SSNSARSFTD VISFNSRLGK PLIDHVHHAQ KPSNFKSSIN LSDNTCKKQG  360
LQTSSPVKMS GRGQGTANES AGKKKRTEDS STSSETVLKK PKQETSAANS SSSSVKMQAP  420
KVKVADKITA LQQIVSPFGK TDTASVLYEA IQYIKFLQDQ IHVQLSSSPY LKTNTHKQDS  480
WGKLDQIRGD HQVKMDLKSR GLCLVPTSCT PQLYSNSQSP ISDVMKRSLD DYEISDDEWE  540
EDHASSFKPS RVLNNKPPPR APPPPAIESF AYKRGRASSA DDADFVVDIS DGSDDDCVEI  600
KDDDLEDDDV EEEVVRSRPV TRGRRFVVED EDSDGDWAEL ESSSEEEEEE EAEAVGDDDV  660
VGRALQKCAK ISADLKRELH GSSAAATASD RYAEVDASSV RIVTQDDINE ACRSDQSDFL  720
PVLKPYQLVG VNFLLLLYRK GIGGAILADE MGLGKTIQAV TYLMLLKHLH KDPGPHLIVC  780
PASVLENWER ELKKWCPSFS VLQYHGAARS AYSRELTSLA KAGMPPPFNV ILVCYSLFER  840
HSAQQKDDRK ILKRWRWSCV LMDEAHALKD KNSYRWKNLM SVARSANQRL MLTGTPLQND  900
LHASFIVLVT PLSLGLDTLS RTLSSHLLFL SELWSMLEFI MPDLFTTEDV DLKKLLSTAD  960
TDLISRMKSI LGPFILRRLK SDVMQQLVPK IQRVEYVIME KEQNDAYKEA IEEYRAASRA  1020
RIAKTSQANT NSIIGVIPRR QISNYFVQFR KIANHPLLVR RIYSDEDVVR FARKLHPMGA  1080
FGFECTLDRV IEEMKSFNDF SIHRLLLSYD ITDKKGCLPD EDVMLSAKSQ ALAELLPILK  1140
QAGHRVLIFS QWTSMLDILE WALDVIGVTY RRLDGSTQVT ERQTIVDTFN NDTSIFACLL  1200
STRAGGQGLN LTGADTVVIH DMDFNPQIDR QAEDRCHRIG QTKPVTIYRL VTKGTVDENV  1260
YEIAKRKLVL DAAVLESGLE MENEGAASEK TMGEILSKLL LG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5jxr_A	6e-80	723	1278	106	562	Chromatin-remodeling complex ATPase-like protein
5jxr_B	6e-80	723	1278	106	562	Chromatin-remodeling complex ATPase-like protein
6ne3_W	7e-82	723	1276	15	466	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	DNA helicase that possesses intrinsic ATP-dependent nucleosome-remodeling activity and is both required for DNA repair and heterochromatin organization. Promotes DNA end resection of double-strand breaks (DSBs) following DNA damage: probably acts by weakening histone DNA interactions in nucleosomes flanking DSBs (By similarity). Probable chromatin remodeling factor. Probable helicase-like transcription factor involved in transcriptional gene silencing. Associates with SUVR2 and contributes to transcriptional gene silencing at RNA-directed DNA methylation (RdDM) target loci but also at RdDM-independent target loci. May be involved in nucleosome positioning to form ordered nucleosome arrays on chromatin (PubMed:25420628). {ECO:0000250\|UniProtKB:P31380, ECO:0000269\|PubMed:25420628, ECO:0000303\|PubMed:16547115}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	mrna00901.1-v1.0-hybrid

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By UV-C illumination (PubMed:15053760). Accumulates in response to the mutagens rose Bengal (RB) and methyl methane sulfonate (MMS) (PubMed:15133154). {ECO:0000269\|PubMed:15053760, ECO:0000269\|PubMed:15133154}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004298634.1	0.0	PREDICTED: protein CHROMATIN REMODELING 19
Swissprot	Q9ZUL5	0.0	CHR19_ARATH; Protein CHROMATIN REMODELING 19
TrEMBL	A0A2P6R4F9	0.0	A0A2P6R4F9_ROSCH; Putative DNA helicase chromatin remodeling SNF2 family
STRING	XP_004298634.1	0.0	(Fragaria vesca)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G31050.1	5e-34	bHLH family protein

Link Out ? help Back to Top
Phytozome	mrna00901.1-v1.0-hybrid

Publications ? help Back to Top
Filkowski J,Kovalchuk O,Kovalchuk I Genome stability of vtc1, tt4, and tt5 Arabidopsis thaliana mutants impaired in protection against oxidative stress. Plant J., 2004. 38(1): p. 60-9 [PMID:15053760] Kovalchuk I,Abramov V,Pogribny I,Kovalchuk O Molecular aspects of plant adaptation to life in the Chernobyl zone. Plant Physiol., 2004. 135(1): p. 357-63 [PMID:15133154] Shaked H,Avivi-Ragolsky N,Levy AA Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination. Genetics, 2006. 173(2): p. 985-94 [PMID:16547115] Xu R,Zhang S,Huang J,Zheng C Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa. PLoS ONE, 2013. 8(11): p. e78982 [PMID:24265739] Han YF, et al. SUVR2 is involved in transcriptional gene silencing by associating with SNF2-related chromatin-remodeling proteins in Arabidopsis. Cell Res., 2014. 24(12): p. 1445-65 [PMID:25420628]