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Histone-lysine N-methyltransferase ATXR5 (EC 2.1.1.43) (Protein SET DOMAIN GROUP 15) (Trithorax-related protein 5) (TRX-related protein 5)

 ATXR5_ARATH             Reviewed;         379 AA.
Q8VZJ1; F4KFB9; Q1AJM5; Q9FXW6; Q9LXE2;
02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
14-MAY-2014, sequence version 2.
25-APR-2018, entry version 121.
RecName: Full=Histone-lysine N-methyltransferase ATXR5;
EC=2.1.1.43;
AltName: Full=Protein SET DOMAIN GROUP 15;
AltName: Full=Trithorax-related protein 5;
Short=TRX-related protein 5;
Flags: Precursor;
Name=ATXR5; Synonyms=SDG15, SET15; OrderedLocusNames=At5g09790;
ORFNames=17I14.20, MTH16.26;
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] (ISOFORM 1), ALTERNATIVE SPLICING,
INTERACTION WITH PCNA1 AND PCNA2, TISSUE SPECIFICITY, AND SUBCELLULAR
LOCATION.
PubMed=16771839; DOI=10.1111/j.1365-313X.2006.02799.x;
Raynaud C., Sozzani R., Glab N., Domenichini S., Perennes C.,
Cella R., Kondorosi E., Bergounioux C.;
"Two cell-cycle regulated SET-domain proteins interact with
proliferating cell nuclear antigen (PCNA) in Arabidopsis.";
Plant J. 47:395-407(2006).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10470850; DOI=10.1093/dnares/6.3.183;
Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Kotani H.,
Miyajima N., Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 5. IX.
Sequence features of the regions of 1,011,550 bp covered by seventeen
P1 and TAC clones.";
DNA Res. 6:183-195(1999).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130714; DOI=10.1038/35048507;
Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K.,
Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S.,
Nakazaki N., Naruo K., Okumura S., Shinpo S., Takeuchi C., Wada T.,
Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M.,
Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R.,
Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J.,
Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M.,
Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M.,
Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P.,
Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C.,
Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N.,
Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J.,
Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S.,
Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W.,
Ramsperger U., Wedler H., Balke K., Wedler E., Peters S.,
van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R.,
Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S.,
Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W.,
Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H.,
Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.;
"Sequence and analysis of chromosome 5 of the plant Arabidopsis
thaliana.";
Nature 408:823-826(2000).
[4]
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).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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).
[6]
NOMENCLATURE.
PubMed=11691919; DOI=10.1093/nar/29.21.4319;
Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K.,
Assalkhou R., Schulz I., Reuter G., Aalen R.B.;
"The Arabidopsis thaliana genome contains at least 29 active genes
encoding SET domain proteins that can be assigned to four
evolutionarily conserved classes.";
Nucleic Acids Res. 29:4319-4333(2001).
[7]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=19503079; DOI=10.1038/nsmb.1611;
Jacob Y., Feng S., LeBlanc C.A., Bernatavichute Y.V., Stroud H.,
Cokus S., Johnson L.M., Pellegrini M., Jacobsen S.E., Michaels S.D.;
"ATXR5 and ATXR6 are H3K27 monomethyltransferases required for
chromatin structure and gene silencing.";
Nat. Struct. Mol. Biol. 16:763-768(2009).
[8]
INTERACTION WITH IPS1.
PubMed=19812700; DOI=10.1371/journal.pone.0007364;
Meng P.H., Raynaud C., Tcherkez G., Blanchet S., Massoud K.,
Domenichini S., Henry Y., Soubigou-Taconnat L., Lelarge-Trouverie C.,
Saindrenan P., Renou J.P., Bergounioux C.;
"Crosstalks between myo-inositol metabolism, programmed cell death and
basal immunity in Arabidopsis.";
PLoS ONE 4:E7364-E7364(2009).
[9]
FUNCTION, AND INTERACTION WITH HTR1.
PubMed=20631708; DOI=10.1038/nature09290;
Jacob Y., Stroud H., Leblanc C., Feng S., Zhuo L., Caro E., Hassel C.,
Gutierrez C., Michaels S.D., Jacobsen S.E.;
"Regulation of heterochromatic DNA replication by histone H3 lysine 27
methyltransferases.";
Nature 466:987-991(2010).
[10]
FUNCTION.
PubMed=22549957; DOI=10.1101/gad.182865.111;
Pontvianne F., Blevins T., Chandrasekhara C., Feng W., Stroud H.,
Jacobsen S.E., Michaels S.D., Pikaard C.S.;
"Histone methyltransferases regulating rRNA gene dose and dosage
control in Arabidopsis.";
Genes Dev. 26:945-957(2012).
[11]
SUBSTRATE SPECIFICITY.
PubMed=24626927; DOI=10.1126/science.1248357;
Jacob Y., Bergamin E., Donoghue M.T., Mongeon V., LeBlanc C.,
Voigt P., Underwood C.J., Brunzelle J.S., Michaels S.D., Reinberg D.,
Couture J.F., Martienssen R.A.;
"Selective methylation of histone H3 variant H3.1 regulates
heterochromatin replication.";
Science 343:1249-1253(2014).
-!- FUNCTION: Histone methyltransferase that specifically
monomethylates 'Lys-37' of histone H3 (H3K27me1). Has much higher
activity on nucleosomes containing H3.1 than H3.3. Involved in the
formation of constitutive heterochromatin and the silencing of
heterochromatic elements. Influences which sets of rRNA gene
variants are expressed or silenced. {ECO:0000269|PubMed:19503079,
ECO:0000269|PubMed:20631708, ECO:0000269|PubMed:22549957}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] =
S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
-!- SUBUNIT: Isoform 1 but not isoform 2 interacts with PCNA1 and
PCNA2. Interacts (via PHD domain) with HTR1 (via N-terminus).
Isoform 2 interacts with IPS1. {ECO:0000269|PubMed:16771839,
ECO:0000269|PubMed:19812700, ECO:0000269|PubMed:20631708}.
-!- INTERACTION:
Q9FEN9:SHL; NbExp=3; IntAct=EBI-15200822, EBI-4458733;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16771839}.
Plastid, chloroplast {ECO:0000269|PubMed:16771839}. Note=Never
found in plastids and the nucleus within the same cell.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q8VZJ1-2; Sequence=Displayed;
Note=Major isoform.;
Name=2;
IsoId=Q8VZJ1-1; Sequence=VSP_054858;
-!- TISSUE SPECIFICITY: Expressed in leaves, roots, stems, flowers,
siliques and developing pollen. Up-regulated in tissues where cell
division is active. {ECO:0000269|PubMed:16771839}.
-!- DISRUPTION PHENOTYPE: No visible phenotype. Atxr5 and atxr6 double
mutant is smaller than wild-type plants, shows partial
decondensation of the chromocenter, decreased H3K27
monomethylation and increased DNA re-replication.
{ECO:0000269|PubMed:19503079}.
-!- MISCELLANEOUS: The binding to histone H3.2 is unaffected by mono-,
di, or trimethylation at H3K9, but is strongly reduced by
increasing levels of H3K4 methylation.
{ECO:0000305|PubMed:20631708}.
-!- SIMILARITY: Belongs to the class V-like SAM-binding
methyltransferase superfamily. Histone-lysine methyltransferase
family. TRX/MLL subfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
-!- SEQUENCE CAUTION:
Sequence=BAB09537.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution (CC BY 4.0) License
-----------------------------------------------------------------------
EMBL; DQ074689; AAZ31374.1; -; mRNA.
EMBL; AB020752; BAB09537.1; ALT_SEQ; Genomic_DNA.
EMBL; AL353994; CAB89351.1; -; Genomic_DNA.
EMBL; CP002688; AED91447.1; -; Genomic_DNA.
EMBL; AY064131; AAL36039.1; -; mRNA.
EMBL; AY120701; AAM52244.1; -; mRNA.
PIR; T49919; T49919.
RefSeq; NP_001078559.1; NM_001085090.2. [Q8VZJ1-2]
RefSeq; NP_001318519.1; NM_001343068.1.
UniGene; At.27076; -.
ProteinModelPortal; Q8VZJ1; -.
SMR; Q8VZJ1; -.
BioGrid; 16117; 7.
DIP; DIP-48529N; -.
IntAct; Q8VZJ1; 11.
STRING; 3702.AT5G09790.2; -.
PaxDb; Q8VZJ1; -.
PRIDE; Q8VZJ1; -.
EnsemblPlants; AT5G09790.2; AT5G09790.2; AT5G09790. [Q8VZJ1-2]
GeneID; 830839; -.
Gramene; AT5G09790.2; AT5G09790.2; AT5G09790. [Q8VZJ1-2]
KEGG; ath:AT5G09790; -.
Araport; AT5G09790; -.
TAIR; locus:2144841; AT5G09790.
eggNOG; KOG1083; Eukaryota.
eggNOG; COG2940; LUCA.
HOGENOM; HOG000238747; -.
InParanoid; Q8VZJ1; -.
OMA; DELTYMP; -.
OrthoDB; EOG09360KQ7; -.
PRO; PR:Q8VZJ1; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q8VZJ1; baseline and differential.
Genevisible; Q8VZJ1; AT.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
GO; GO:0005634; C:nucleus; IDA:TAIR.
GO; GO:0046976; F:histone methyltransferase activity (H3-K27 specific); IDA:TAIR.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0009294; P:DNA mediated transformation; IMP:TAIR.
GO; GO:0070734; P:histone H3-K27 methylation; IDA:TAIR.
GO; GO:0009555; P:pollen development; IMP:TAIR.
GO; GO:0051726; P:regulation of cell cycle; IEP:TAIR.
GO; GO:0006275; P:regulation of DNA replication; IGI:TAIR.
Gene3D; 3.30.40.10; -; 1.
InterPro; IPR001214; SET_dom.
InterPro; IPR019786; Zinc_finger_PHD-type_CS.
InterPro; IPR011011; Znf_FYVE_PHD.
InterPro; IPR001965; Znf_PHD.
InterPro; IPR019787; Znf_PHD-finger.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
Pfam; PF00628; PHD; 1.
Pfam; PF00856; SET; 1.
SMART; SM00249; PHD; 1.
SMART; SM00317; SET; 1.
SUPFAM; SSF57903; SSF57903; 1.
PROSITE; PS50280; SET; 1.
PROSITE; PS01359; ZF_PHD_1; 1.
PROSITE; PS50016; ZF_PHD_2; 1.
1: Evidence at protein level;
Alternative splicing; Chloroplast; Chromatin regulator;
Complete proteome; Metal-binding; Methyltransferase; Nucleus; Plastid;
Reference proteome; S-adenosyl-L-methionine; Transferase;
Transit peptide; Zinc; Zinc-finger.
TRANSIT 1 44 Chloroplast. {ECO:0000255}.
CHAIN 45 379 Histone-lysine N-methyltransferase ATXR5.
/FTId=PRO_0000429173.
DOMAIN 245 367 SET. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
ZN_FING 64 114 PHD-type. {ECO:0000255|PROSITE-
ProRule:PRU00146}.
REGION 255 257 S-adenosyl-L-methionine binding.
{ECO:0000250}.
REGION 317 321 S-adenosyl-L-methionine binding.
{ECO:0000250}.
REGION 369 370 substrate binding. {ECO:0000250}.
MOTIF 122 129 PIP motif.
COMPBIAS 52 59 Poly-Glu.
BINDING 221 221 Substrate. {ECO:0000250}.
BINDING 339 339 Substrate. {ECO:0000250}.
BINDING 366 366 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
BINDING 373 373 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
VAR_SEQ 120 146 Missing (in isoform 2).
{ECO:0000303|PubMed:14593172}.
/FTId=VSP_054858.
CONFLICT 347 347 R -> P (in Ref. 1; AAZ31374).
{ECO:0000305}.
SEQUENCE 379 AA; 43034 MW; F5A792C7E491BB48 CRC64;
MATWNASSPA ASPCSSRRRT KAPARRPSSE SPPPRKMKSM AEIMAKSVPV VEQEEEEDED
SYSNVTCEKC GSGEGDDELL LCDKCDRGFH MKCLRPIVVR VPIGTWLCVD CSDQRPVRRL
SQKKILHFFR IEKHTHQTDK LELSQEETRK RRRSCSLTVK KRRRKLLPLV PSEDPDQRLA
QMGTLASALT ALGIKYSDGL NYVPGMAPRS ANQSKLEKGG MQVLCKEDLE TLEQCQSMYR
RGECPPLVVV FDPLEGYTVE ADGPIKDLTF IAEYTGDVDY LKNREKDDCD SIMTLLLSED
PSKTLVICPD KFGNISRFIN GINNHNPVAK KKQNCKCVRY SINGECRVLL VATRDISKGE
RLYYDYNGYE HEYPTHHFL


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