PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID FANhyb_rscf00000052.1.g00021.1
Organism
Fragaria x ananassa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria
Family B3
Protein Properties Length: 1043aa    MW: 116844 Da    PI: 10.1847
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
FANhyb_rscf00000052.1.g00021.1genomekazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B349.67.2e-16155232285
                                     EEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS
                              B3   2 fkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 
                                     +k ++ s+v++  +l lpk+f++++  +k++s + tlede+g +++v +     ++r+ l++GWk+F++ ++L egD +
  FANhyb_rscf00000052.1.g00021.1 155 VKSMVYSHVSRVFWLGLPKDFCDANL-VKKKS-DRTLEDEHGDQFTVVY----IPERHGLSGGWKKFAQKKKLHEGDAI 227
                                     688999****************9994.33344.799*************....455566******************** PP

                                     EEEE- CS
                              B3  81 vFkld 85 
                                     vF+++
  FANhyb_rscf00000052.1.g00021.1 228 VFQRT 232
                                     ***43 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.94E-18149236IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.1E-15149235IPR015300DNA-binding pseudobarrel domain
CDDcd100172.93E-19152233No hitNo description
PROSITE profilePS5086310.306154245IPR003340B3 DNA binding domain
SMARTSM010191.5E-11154243IPR003340B3 DNA binding domain
PfamPF023623.4E-14155232IPR003340B3 DNA binding domain
Gene3DG3DSA:2.170.11.105.1E-54525547IPR013030DNA topoisomerase I, DNA binding, mixed alpha/beta motif, eukaryotic-type
SuperFamilySSF567412.88E-92525744IPR008336DNA topoisomerase I, DNA binding, eukaryotic-type
CDDcd006601.56E-97533744No hitNo description
PfamPF029191.0E-89533744IPR008336DNA topoisomerase I, DNA binding, eukaryotic-type
Gene3DG3DSA:1.10.10.411.2E-34548631IPR013034DNA topoisomerase I, domain 1
Gene3DG3DSA:2.170.11.105.1E-54633744IPR013030DNA topoisomerase I, DNA binding, mixed alpha/beta motif, eukaryotic-type
PRINTSPR004162.6E-31673682IPR001631DNA topoisomerase I
SMARTSM004351.0E-1496731016IPR013499DNA topoisomerase I, eukaryotic-type
PRINTSPR004162.6E-31754773IPR001631DNA topoisomerase I
SuperFamilySSF563498.95E-59765915IPR011010DNA breaking-rejoining enzyme, catalytic core
PfamPF010281.3E-61766938IPR013500DNA topoisomerase I, catalytic core, eukaryotic-type
Gene3DG3DSA:3.90.15.101.9E-30767854IPR014711DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type
PRINTSPR004162.6E-31778792IPR001631DNA topoisomerase I
PRINTSPR004162.6E-31800816IPR001631DNA topoisomerase I
PRINTSPR004162.6E-31858872IPR001631DNA topoisomerase I
Gene3DG3DSA:1.10.132.101.6E-598621043IPR014727DNA topoisomerase I, catalytic core, alpha/beta subdomain
PfamPF143702.1E-289751043IPR025834Topoisomerase I C-terminal domain
SuperFamilySSF563498.95E-599911040IPR011010DNA breaking-rejoining enzyme, catalytic core
PRINTSPR004162.6E-319961007IPR001631DNA topoisomerase I
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006265Biological ProcessDNA topological change
GO:0005694Cellular Componentchromosome
GO:0003677Molecular FunctionDNA binding
GO:0003917Molecular FunctionDNA topoisomerase type I activity
GO:0003918Molecular FunctionDNA topoisomerase type II (ATP-hydrolyzing) activity
Sequence ? help Back to Top
Protein Sequence    Length: 1043 aa     Download sequence    Send to blast
MLWSLKPNGV HRKYREIKTR CSIHDPPQRR KIMLDSSKKS KNKEKTSSKA PPSLRKHKIV  60
EQSRGTFVEV DISSPVKPIA LKVKISPPPS PRPKTKSTAP STQRIKSTPS IPGTKRKNVL  120
VREEPTNASD AARSAAYEAA KAHQMGLASS TPSIVKSMVY SHVSRVFWLG LPKDFCDANL  180
VKKKSDRTLE DEHGDQFTVV YIPERHGLSG GWKKFAQKKK LHEGDAIVFQ RTEPKRLKGY  240
GPGSDQALPG GGGQVAGGPA VRRRRGGPGR IVDGGGVLHE GRDSALEPAR RQAGEGGAGP  300
AAEPVSDAVL VLRRKHFRRR AEGAAGLAGA GGHGGEAEEG EGDAEEHAQL LDGGLRRKRR  360
FSVVIVFVIG FTSGKTSSPV LSSDQSKQFQ EQTMPSASVE HFAPAVENSD SDDDKPLSSR  420
YLKGKGEIPK RPLDHQTNIS EQSEPKKAKL SGSSLPFKNE QVLSSAKQEP QVDYDDITLA  480
QRMKKTRSVN KPSTRTEQKV PKISSSSKMI KKGKEPDKAS KDHASSKSDN KQKWTSLVHN  540
GVIFPPPYEP HGVKMLYNGK PVDLTPEQEE VATMFALMTD TDYVRKQRFR DNFWMDWRKL  600
LGEKHVIQEL DACDFQPIYE WWCQEKEKKK QLSAEEKKAA KEEKSKQEEK YKWAIIDGVK  660
EEVQSFRVEP PGLFRGRGEQ PQSGRLKRRI IPSDITINIG EDAPTPECPI PGQNWKRIRH  720
DNTVSWLACW DDPIFEEKTK YVMLGSSSSL RGQNSSSYLS YRQICAKRDG NEKDVDEEAD  780
TVGCCTLKVE NVKAIAPNLL EFDFLGKDSI RYHQTHQVDL PVYNAIKQFQ KGKSSSDKLF  840
DQLDTTILNA SLKEMMPGLT TKVFRTYNAS ITLDNMLNEK TKKEADVSAR VAVYNNANKK  900
VAILCNHQRA EAKTFGEQIS KLNKKIEDLK GVMKALETDL VRAREGKSPL KDGDGKQKRN  960
LTPEALEKKM AQTTKNIETI ERKIADKEDK KNVATETSKT NYLDPRITVA WCKRHEVPIQ  1020
KMYSKIQLKK FAWAMDAHPD FRF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a31_A1e-133533104342591PROTEIN (TOPOISOMERASE I)
1k4s_A1e-133533104343592DNA topoisomerase I
1k4t_A1e-133533104343592DNA topoisomerase I
1sc7_A1e-133533104343592DNA topoisomerase I
1t8i_A1e-133533104343592DNA topoisomerase I
1tl8_A1e-133533104343592DNA topoisomerase I
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtReleases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free DNA strand then rotates around the intact phosphodiester bond on the opposing strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Topoisomerases 1 enzymes (TOP1A and TOP1B) are essential for plant survival (PubMed:12215507). {ECO:0000250|UniProtKB:P11387, ECO:0000269|PubMed:12215507}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004293195.10.0PREDICTED: DNA topoisomerase 1-like
SwissprotQ9FJ790.0TOP1B_ARATH; DNA topoisomerase 1 beta
TrEMBLA0A2P6PYY20.0A0A2P6PYY2_ROSCH; DNA topoisomerase I
STRINGXP_004293195.10.0(Fragaria vesca)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G58280.16e-21B3 family protein
Publications ? help Back to Top
  1. Takahashi T,Matsuhara S,Abe M,Komeda Y
    Disruption of a DNA topoisomerase I gene affects morphogenesis in Arabidopsis.
    Plant Cell, 2002. 14(9): p. 2085-93
    [PMID:12215507]
  2. Dinh TT, et al.
    DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis.
    PLoS Genet., 2014. 10(7): p. e1004446
    [PMID:24992598]
  3. Zhang Y, et al.
    TOPOISOMERASE1α Acts through Two Distinct Mechanisms to Regulate Stele and Columella Stem Cell Maintenance.
    Plant Physiol., 2016. 171(1): p. 483-93
    [PMID:26969721]
  4. Gong X,Shen L,Peng YZ,Gan Y,Yu H
    DNA Topoisomerase Iα Affects the Floral Transition.
    Plant Physiol., 2017. 173(1): p. 642-654
    [PMID:27837087]
  5. Gao C, et al.
    Functional characterization of Brassica napus DNA topoisomerase Iα-1 and its effect on flowering time when expressed in Arabidopsis thaliana.
    Biochem. Biophys. Res. Commun., 2017. 486(1): p. 124-129
    [PMID:28283390]
  6. Sabatini ME,Pagano A,Araùjo S,Balestrazzi A,Macovei A
    The Tyrosyl-DNA Phosphodiesterase 1β (Tdp1β) Gene Discloses an Early Response to Abiotic Stresses.
    Genes (Basel), 2018.
    [PMID:29099800]