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Serrate RNA effector molecule

 SRRT_ARATH              Reviewed;         720 AA.
Q9ZVD0; Q93W84;
22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
01-JUN-2002, sequence version 2.
07-NOV-2018, entry version 144.
RecName: Full=Serrate RNA effector molecule;
Name=SE; OrderedLocusNames=At2g27100; ORFNames=T20P8.15;
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], TISSUE SPECIFICITY, AND DISRUPTION
PHENOTYPE.
STRAIN=cv. Columbia;
PubMed=11402159; DOI=10.1105/tpc.13.6.1263;
Prigge M.J., Wagner D.R.;
"The arabidopsis serrate gene encodes a zinc-finger protein required
for normal shoot development.";
Plant Cell 13:1263-1279(2001).
[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.
PubMed=16222298; DOI=10.1038/nature04052;
Grigg S.P., Canales C., Hay A., Tsiantis M.;
"SERRATE coordinates shoot meristem function and leaf axial patterning
in Arabidopsis.";
Nature 437:1022-1026(2005).
[6]
FUNCTION, INTERACTION WITH HYL1, AND DISRUPTION PHENOTYPE.
PubMed=16977334; DOI=10.1038/sj.embor.7400806;
Lobbes D., Rallapalli G., Schmidt D.D., Martin C., Clarke J.;
"SERRATE: a new player on the plant microRNA scene.";
EMBO Rep. 7:1052-1058(2006).
[7]
FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH HYL1.
PubMed=16889646; DOI=10.1111/j.1365-313X.2006.02835.x;
Yang L., Liu Z., Lu F., Dong A., Huang H.;
"SERRATE is a novel nuclear regulator in primary microRNA processing
in Arabidopsis.";
Plant J. 47:841-850(2006).
[8]
SUBCELLULAR LOCATION.
PubMed=17442570; DOI=10.1016/j.cub.2007.04.005;
Fang Y., Spector D.L.;
"Identification of nuclear dicing bodies containing proteins for
microRNA biogenesis in living Arabidopsis plants.";
Curr. Biol. 17:818-823(2007).
[9]
SUBCELLULAR LOCATION.
PubMed=17675322; DOI=10.1093/pcp/pcm099;
Fujioka Y., Utsumi M., Ohba Y., Watanabe Y.;
"Location of a possible miRNA processing site in SmD3/SmB nuclear
bodies in Arabidopsis.";
Plant Cell Physiol. 48:1243-1253(2007).
[10]
FUNCTION.
PubMed=18632569; DOI=10.1073/pnas.0803356105;
Dong Z., Han M.-H., Fedoroff N.;
"The RNA-binding proteins HYL1 and SE promote accurate in vitro
processing of pri-miRNA by DCL1.";
Proc. Natl. Acad. Sci. U.S.A. 105:9970-9975(2008).
[11]
FUNCTION.
PubMed=18550839; DOI=10.1073/pnas.0802493105;
Laubinger S., Sachsenberg T., Zeller G., Busch W., Lohmann J.U.,
Raetsch G., Weigel D.;
"Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA
splicing and microRNA processing in Arabidopsis thaliana.";
Proc. Natl. Acad. Sci. U.S.A. 105:8795-8800(2008).
[12]
SUBCELLULAR LOCATION, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT
SER-689, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
STRAIN=cv. Columbia;
PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A.,
Andreasson E., Rathjen J.P., Peck S.C.;
"Phosphoproteomic analysis of nuclei-enriched fractions from
Arabidopsis thaliana.";
J. Proteomics 72:439-451(2009).
[13]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-76; SER-90 AND SER-92,
AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19376835; DOI=10.1104/pp.109.138677;
Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
Grossmann J., Gruissem W., Baginsky S.;
"Large-scale Arabidopsis phosphoproteome profiling reveals novel
chloroplast kinase substrates and phosphorylation networks.";
Plant Physiol. 150:889-903(2009).
[14]
INTERACTION WITH RCF3; RS40 AND RS41, AND SUBCELLULAR LOCATION.
PubMed=26227967; DOI=10.1093/nar/gkv751;
Chen T., Cui P., Xiong L.;
"The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40
and RS41 participate in miRNA biogenesis in Arabidopsis.";
Nucleic Acids Res. 43:8283-8298(2015).
[15]
X-RAY CRYSTALLOGRAPHY (2.74 ANGSTROMS) OF 194-543.
PubMed=21685453; DOI=10.1093/nar/gkr428;
Machida S., Chen H.Y., Adam Yuan Y.;
"Molecular insights into miRNA processing by Arabidopsis thaliana
SERRATE.";
Nucleic Acids Res. 39:7828-7836(2011).
-!- FUNCTION: Acts as a mediator between the cap-binding complex (CBC)
and both the pre-mRNA splicing and primary microRNAs (miRNAs)
processing machinery. Required for proper processing of primary
miRNAs to miRNAs, thereby playing a role in RNA-mediated gene
silencing (RNAi) by miRNAs. Does not participate in sense post-
transcriptional gene silencing. Acts as a regulator of meristem
activity and adaxial leaf fate via the miRNA gene-silencing
pathway by regulating the expression of PHB and by limiting the
competence of shoot tissue to respond to KNOX expression. Its
function is however not limited to miRNA-mediated repression of
leaf polarity genes, but rather acts as a general regulator of
primary microRNAs processing. Also critical for the accumulation
of the trans-acting small interfering RNA (ta-siRNA). Required for
pre-mRNA splicing. {ECO:0000269|PubMed:16222298,
ECO:0000269|PubMed:16889646, ECO:0000269|PubMed:16977334,
ECO:0000269|PubMed:18550839, ECO:0000269|PubMed:18632569}.
-!- SUBUNIT: Interacts with HYL1 (PubMed:16889646, PubMed:16977334).
Interacts with RCF3, RS40 and RS41 (PubMed:26227967).
{ECO:0000269|PubMed:16889646, ECO:0000269|PubMed:16977334,
ECO:0000269|PubMed:26227967}.
-!- INTERACTION:
Q6EVK6:BRM; NbExp=6; IntAct=EBI-6553299, EBI-2025535;
Q5YDB6:CPL1; NbExp=7; IntAct=EBI-6553299, EBI-1786459;
O04492:DRB1; NbExp=7; IntAct=EBI-6553299, EBI-632620;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16889646,
ECO:0000269|PubMed:17442570, ECO:0000269|PubMed:17675322,
ECO:0000269|PubMed:19245862}. Nucleus speckle
{ECO:0000269|PubMed:26227967}. Note=Localizes to nuclear dicing
body (also named D body), a nuclear body distributed throughout
the nucleoplasm involved in miRNA processing.
-!- TISSUE SPECIFICITY: Expressed in shoot meristems and in emerging
organ primordia throughout development.
{ECO:0000269|PubMed:11402159}.
-!- DISRUPTION PHENOTYPE: Death during embryogenesis. Weaker mutants
(se-1, se-2 and se-3) also exist. Mutant se-1 displays defects in
shoot and leaf development. Mutants se-2 and se-3 show adaxial
leaf curling, loss of asymmetric differentiation of abaxial and
adaxial cell types and development of trumpet-shaped or radial
leaves. Vascular polarity of se-3 leaves is also perturbed, with
xylem elements forming both adaxially and abaxially in the
vascular bundle. {ECO:0000269|PubMed:11402159,
ECO:0000269|PubMed:16977334}.
-!- SIMILARITY: Belongs to the ARS2 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF311221; AAK63206.1; -; mRNA.
EMBL; AC005623; AAC77868.2; -; Genomic_DNA.
EMBL; CP002685; AEC07936.1; -; Genomic_DNA.
EMBL; AF428305; AAL16137.1; -; mRNA.
EMBL; AY039915; AAK64019.1; -; mRNA.
EMBL; AY142569; AAN13138.1; -; mRNA.
EMBL; AY143937; AAN28876.1; -; mRNA.
PIR; G84668; G84668.
RefSeq; NP_565635.1; NM_128268.3.
UniGene; At.25511; -.
PDB; 3AX1; X-ray; 2.74 A; A=194-543.
PDBsum; 3AX1; -.
ProteinModelPortal; Q9ZVD0; -.
SMR; Q9ZVD0; -.
BioGrid; 2604; 12.
DIP; DIP-58979N; -.
IntAct; Q9ZVD0; 5.
STRING; 3702.AT2G27100.1; -.
iPTMnet; Q9ZVD0; -.
PaxDb; Q9ZVD0; -.
PRIDE; Q9ZVD0; -.
EnsemblPlants; AT2G27100.1; AT2G27100.1; AT2G27100.
GeneID; 817252; -.
Gramene; AT2G27100.1; AT2G27100.1; AT2G27100.
KEGG; ath:AT2G27100; -.
Araport; AT2G27100; -.
TAIR; locus:2059294; AT2G27100.
eggNOG; KOG2295; Eukaryota.
eggNOG; ENOG410XR8S; LUCA.
HOGENOM; HOG000082562; -.
InParanoid; Q9ZVD0; -.
OMA; NQFPPFR; -.
OrthoDB; EOG0936071Q; -.
PhylomeDB; Q9ZVD0; -.
EvolutionaryTrace; Q9ZVD0; -.
PRO; PR:Q9ZVD0; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; Q9ZVD0; baseline and differential.
Genevisible; Q9ZVD0; AT.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:0005846; C:nuclear cap binding complex; IPI:TAIR.
GO; GO:0010445; C:nuclear dicing body; IDA:UniProtKB.
GO; GO:0016607; C:nuclear speck; IDA:TAIR.
GO; GO:0005730; C:nucleolus; IDA:TAIR.
GO; GO:0005634; C:nucleus; IDA:TAIR.
GO; GO:0003677; F:DNA binding; ISS:TAIR.
GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
GO; GO:0031053; P:primary miRNA processing; IMP:UniProtKB.
GO; GO:0010267; P:production of ta-siRNAs involved in RNA interference; IMP:TAIR.
GO; GO:2000011; P:regulation of adaxial/abaxial pattern formation; IMP:TAIR.
GO; GO:0000381; P:regulation of alternative mRNA splicing, via spliceosome; IMP:TAIR.
GO; GO:0048509; P:regulation of meristem development; IMP:TAIR.
GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
GO; GO:0008380; P:RNA splicing; IMP:UniProtKB.
GO; GO:0048367; P:shoot system development; IMP:TAIR.
InterPro; IPR039727; SE/Ars2.
InterPro; IPR007042; SERRATE/Ars2_C.
InterPro; IPR021933; SERRATE/Ars2_N.
InterPro; IPR013087; Znf_C2H2_type.
PANTHER; PTHR13165; PTHR13165; 1.
Pfam; PF04959; ARS2; 1.
Pfam; PF12066; DUF3546; 1.
PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Metal-binding; mRNA processing;
mRNA splicing; Nucleus; Phosphoprotein; Reference proteome;
RNA-mediated gene silencing; Zinc; Zinc-finger.
CHAIN 1 720 Serrate RNA effector molecule.
/FTId=PRO_0000385228.
ZN_FING 498 523 C2H2-type.
COMPBIAS 25 111 Pro-rich.
COMPBIAS 121 182 Gly-rich.
COMPBIAS 562 598 Arg-rich.
COMPBIAS 629 690 Pro-rich.
MOD_RES 76 76 Phosphoserine.
{ECO:0000244|PubMed:19376835}.
MOD_RES 90 90 Phosphoserine.
{ECO:0000244|PubMed:19376835}.
MOD_RES 92 92 Phosphoserine.
{ECO:0000244|PubMed:19376835}.
MOD_RES 689 689 Phosphoserine.
{ECO:0000244|PubMed:19245862}.
HELIX 198 201 {ECO:0000244|PDB:3AX1}.
HELIX 202 204 {ECO:0000244|PDB:3AX1}.
TURN 205 207 {ECO:0000244|PDB:3AX1}.
HELIX 211 237 {ECO:0000244|PDB:3AX1}.
HELIX 241 247 {ECO:0000244|PDB:3AX1}.
HELIX 249 275 {ECO:0000244|PDB:3AX1}.
STRAND 283 286 {ECO:0000244|PDB:3AX1}.
HELIX 331 333 {ECO:0000244|PDB:3AX1}.
HELIX 336 357 {ECO:0000244|PDB:3AX1}.
STRAND 386 388 {ECO:0000244|PDB:3AX1}.
STRAND 395 397 {ECO:0000244|PDB:3AX1}.
HELIX 400 414 {ECO:0000244|PDB:3AX1}.
HELIX 418 420 {ECO:0000244|PDB:3AX1}.
HELIX 446 460 {ECO:0000244|PDB:3AX1}.
HELIX 464 469 {ECO:0000244|PDB:3AX1}.
HELIX 471 482 {ECO:0000244|PDB:3AX1}.
HELIX 483 485 {ECO:0000244|PDB:3AX1}.
STRAND 486 490 {ECO:0000244|PDB:3AX1}.
STRAND 492 500 {ECO:0000244|PDB:3AX1}.
STRAND 502 504 {ECO:0000244|PDB:3AX1}.
STRAND 508 511 {ECO:0000244|PDB:3AX1}.
HELIX 512 522 {ECO:0000244|PDB:3AX1}.
HELIX 524 543 {ECO:0000244|PDB:3AX1}.
SEQUENCE 720 AA; 81098 MW; 44D7041FAEA4A857 CRC64;
MADVNLPPSD SVDNRLPEKS TSSSPPPPPP SSSLPQQEQE QDQQQLPLRR ERDSRERRDE
RDIERPPPNR RERDRSPLPP PRRDYKRRPS LSPPPPYRDR RHSPPQRRSP PQKRYRRDDN
GYDGRRGSPR GGYGPPDRRF GYDHGGGYDR EMGGRPGYGD ERPHGRFMGR YQDWEGGRGG
YGDASNSGNP QRDGLMSYKQ FIQELEDDIL PSEAERRYQE YKSEYITTQK RAFFNTHKEE
DWLKNKYHPT NLLSVIERRN DLAQKVAKDF LLDLQSGTLD LGPAVTALNK SGRTSEPNSE
DEAAGVGKRK RHGMGGAKEN ELLSAAPKAP SFTSDPKRIL TDVEQTQALV RKLDSEKKIE
ENVLQGSETE KSGREKLHSG STGPVVIIRG LTSVKGLEGV ELLDTLVTYL WRVHGLDYYG
KVETNEAKGL RHVRAEGKVS DAKGDENESK FDSHWQERLK GQDPLEVMAA KEKIDAAATE
ALDPHVRKIR DEKYGWKYGC GAKGCTKLFH AAEFVYKHLK LKHTELVTEL TTKVREELYF
QNYMNDPNAP GGQPATQQSG PRDRPIRRKP SMENRLRDDR GGRRERDGRA NGNDRNDRSE
DQQRGDNDGG NPGEVGYDAF GGQGGVHVPP FLSDINPPPM LMPVPGAGPL GPFVPAPPEV
AMQMFRDPSG PNPPFEGSGR GGPAPFLLSP AFRQDPRRLR SYQDLDAPEE EVTVIDYRSL


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