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E3 ubiquitin-protein ligase RFI2 (EC 2.3.2.27) (Protein RED AND FAR-RED INSENSITIVE 2)

 RFI2_ARATH              Reviewed;         358 AA.
O82239; A0A1P8B018;
07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
01-JUN-2002, sequence version 2.
25-APR-2018, entry version 138.
RecName: Full=E3 ubiquitin-protein ligase RFI2 {ECO:0000303|PubMed:16384903};
EC=2.3.2.27 {ECO:0000269|PubMed:15644464};
AltName: Full=Protein RED AND FAR-RED INSENSITIVE 2 {ECO:0000303|PubMed:16384903};
Name=RFI2 {ECO:0000303|PubMed:16384903};
OrderedLocusNames=At2g47700 {ECO:0000312|Araport:AT2G47700};
ORFNames=F17A22.9 {ECO:0000312|EMBL:AAC63626.2};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, AND GENE FAMILY.
STRAIN=cv. Columbia;
PubMed=15644464; DOI=10.1104/pp.104.052423;
Stone S.L., Hauksdottir H., Troy A., Herschleb J., Kraft E.,
Callis J.;
"Functional analysis of the RING-type ubiquitin ligase family of
Arabidopsis.";
Plant Physiol. 137:13-30(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617197; DOI=10.1038/45471;
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
Venter J.C.;
"Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana.";
Nature 402:761-768(1999).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
FUNCTION, DISRUPTION PHENOTYPE, AND INDUCTION BY CIRCADIAN RYTHM.
STRAIN=cv. Columbia, and cv. Wassilewskija;
PubMed=16709197; DOI=10.1111/j.1365-313X.2006.02740.x;
Chen M., Ni M.;
"RFI2, a RING-domain zinc finger protein, negatively regulates
CONSTANS expression and photoperiodic flowering.";
Plant J. 46:823-833(2006).
[6]
FUNCTION, DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
STRAIN=cv. Columbia, and cv. Wassilewskija;
PubMed=16384903; DOI=10.1104/pp.105.073163;
Chen M., Ni M.;
"RED AND FAR-RED INSENSITIVE 2, a RING-domain zinc finger protein,
mediates phytochrome-controlled seedling deetiolation responses.";
Plant Physiol. 140:457-465(2006).
-!- FUNCTION: Mediates phytochrome (phyA and phyB)-controlled seedling
deetiolation responses such as hypocotyl elongation in response to
red and far-red light (PubMed:16709197, PubMed:16384903). Required
for light-induced expression of LHCB3 and CHALCONE SYNTHASE (CHS)
(PubMed:16384903). Regulates negatively CONSTANS (CO) and
FLOWERING LOCUS T (FT) expression and photoperiodic flowering
(PubMed:16709197). {ECO:0000269|PubMed:16384903,
ECO:0000269|PubMed:16709197}.
-!- CATALYTIC ACTIVITY: S-ubiquitinyl-[E2 ubiquitin-conjugating
enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-
conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor
protein]-L-lysine. {ECO:0000269|PubMed:15644464}.
-!- PATHWAY: Protein modification; protein ubiquitination.
{ECO:0000305|PubMed:15644464}.
-!- INTERACTION:
A9LNK9:CPSF30; NbExp=3; IntAct=EBI-4425094, EBI-962511;
Q84WI0:GIS; NbExp=3; IntAct=EBI-4425094, EBI-15195983;
Q9LXU1:PIM1; NbExp=3; IntAct=EBI-4425094, EBI-15193025;
Q9S7W5:TCP13; NbExp=3; IntAct=EBI-4425094, EBI-4424877;
Q9C9L2:TCP15; NbExp=3; IntAct=EBI-4425094, EBI-4426144;
Q9LVG2:TOE2; NbExp=3; IntAct=EBI-4425094, EBI-4424568;
Q39262:ZFP3; NbExp=3; IntAct=EBI-4425094, EBI-15200178;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16384903}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=O82239-1; Sequence=Displayed;
Name=2;
IsoId=O82239-2; Sequence=VSP_058959, VSP_058960;
Note=Derived from EST data. No experimental confirmation
available. {ECO:0000312|EMBL:ANM62259.1};
-!- INDUCTION: Levels are following a circadian rythm oscillated under
day/night cycles with higher levels during the night.
{ECO:0000269|PubMed:16709197}.
-!- DISRUPTION PHENOTYPE: Photomorphogenic mutant insensitive to red
and far-red light leading to long hypocotyls. Flowers early
particularly under long days (PubMed:16709197, PubMed:16384903).
Also impaired in phytochrome-mediated end-of-day far-red light
response, cotyledon expansion, far-red light block of greening,
and light-induced expression of LHCB3 and CHALCONE SYNTHASE (CHS)
(PubMed:16384903). Enhanced expression of CONSTANS (CO) and
FLOWERING LOCUS T (FT) under long days and short days
(PubMed:16709197). {ECO:0000269|PubMed:16384903,
ECO:0000269|PubMed:16709197}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; DQ086859; AAZ14075.1; -; mRNA.
EMBL; AC005309; AAC63626.2; -; Genomic_DNA.
EMBL; CP002685; AEC10878.1; -; Genomic_DNA.
EMBL; CP002685; ANM62259.1; -; Genomic_DNA.
EMBL; BT002412; AAO00772.1; -; mRNA.
EMBL; BT008845; AAP68284.1; -; mRNA.
PIR; E84918; E84918.
RefSeq; NP_001324431.1; NM_001337272.1. [O82239-2]
RefSeq; NP_850478.1; NM_180147.3. [O82239-1]
UniGene; At.21841; -.
UniGene; At.36327; -.
SMR; O82239; -.
IntAct; O82239; 48.
STRING; 3702.AT2G47700.1; -.
PaxDb; O82239; -.
EnsemblPlants; AT2G47700.1; AT2G47700.1; AT2G47700. [O82239-1]
EnsemblPlants; AT2G47700.2; AT2G47700.2; AT2G47700. [O82239-2]
GeneID; 819383; -.
Gramene; AT2G47700.1; AT2G47700.1; AT2G47700. [O82239-1]
Gramene; AT2G47700.2; AT2G47700.2; AT2G47700. [O82239-2]
KEGG; ath:AT2G47700; -.
Araport; AT2G47700; -.
TAIR; locus:2043438; AT2G47700.
eggNOG; ENOG410JCB4; Eukaryota.
eggNOG; ENOG410Y9QY; LUCA.
HOGENOM; HOG000243234; -.
OMA; QHHANGP; -.
OrthoDB; EOG09360EU1; -.
UniPathway; UPA00143; -.
PRO; PR:O82239; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; O82239; baseline and differential.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:TAIR.
GO; GO:0007623; P:circadian rhythm; IEP:UniProtKB.
GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
GO; GO:0010629; P:negative regulation of gene expression; IMP:UniProtKB.
GO; GO:0009585; P:red, far-red light phototransduction; IEA:UniProtKB-KW.
GO; GO:0010468; P:regulation of gene expression; IMP:UniProtKB.
GO; GO:2000028; P:regulation of photoperiodism, flowering; IMP:UniProtKB.
GO; GO:0090227; P:regulation of red or far-red light signaling pathway; IMP:UniProtKB.
GO; GO:0010218; P:response to far red light; IMP:UniProtKB.
GO; GO:0010114; P:response to red light; IMP:UniProtKB.
Gene3D; 3.30.40.10; -; 1.
InterPro; IPR001841; Znf_RING.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
Pfam; PF13639; zf-RING_2; 1.
SMART; SM00184; RING; 1.
PROSITE; PS50089; ZF_RING_2; 1.
1: Evidence at protein level;
Alternative splicing; Biological rhythms; Complete proteome;
Flowering; Metal-binding; Nucleus; Phytochrome signaling pathway;
Reference proteome; Transferase; Ubl conjugation pathway; Zinc;
Zinc-finger.
CHAIN 1 358 E3 ubiquitin-protein ligase RFI2.
/FTId=PRO_0000440167.
ZN_FING 38 83 RING-type; atypical.
{ECO:0000255|PROSITE-ProRule:PRU00175}.
COMPBIAS 152 212 His-rich. {ECO:0000255|PROSITE-
ProRule:PRU00009}.
COMPBIAS 300 309 Poly-Pro. {ECO:0000255}.
VAR_SEQ 248 272 SNQRSSPAINSYQGSSTQMREQHHA -> LASQTPYCSQLL
AECFTIFFWNWAL (in isoform 2).
/FTId=VSP_058959.
VAR_SEQ 273 358 Missing (in isoform 2).
/FTId=VSP_058960.
SEQUENCE 358 AA; 39937 MW; 2F9689C68B752F79 CRC64;
MAGAKDSGCD DDLRIAGGCD PGKRGNPEDS SSPVEVSCSI CLESVLDDGT RSKAKLQCGH
QFHLDCIGSA FNMKGAMQCP NCRNVEKGQW LYANGSTRPF PEFSMEDWIP EEDLYGLSYP
EMQYRVHWCP FGELSQAAAS FEELEPATTT YHTEFHGHHA AAVNHSYLAY VGPGPAATPR
TSDNNSTDDH PWNSHSNDHF HQLPVAPQYH HHSPSFSLPA AHVVDGEVDS SAARGLPYAH
PFLFSHRSNQ RSSPAINSYQ GSSTQMREQH HAYNHQRQQH HANGPTLASP LISMTRRGLP
PPPPPPPMPD QNVGFFIYPG GHHEPETDQI HAWERDWFPH FPVPSNHRTI PSLWHRHF


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