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Methyl-CpG-binding domain-containing protein 9 (AtMBD9) (MBD09) (EC 2.3.1.48) (Histone acetyl transferase MBD9) (Methyl-CpG-binding protein MBD9)

 MBD9_ARATH              Reviewed;        2176 AA.
Q9SGH2; Q9SSA6;
08-MAR-2011, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
22-NOV-2017, entry version 130.
RecName: Full=Methyl-CpG-binding domain-containing protein 9;
Short=AtMBD9;
Short=MBD09;
EC=2.3.1.48;
AltName: Full=Histone acetyl transferase MBD9;
AltName: Full=Methyl-CpG-binding protein MBD9;
Name=MBD9; OrderedLocusNames=At3g01460; ORFNames=F4P13.1, T13O15.10;
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 [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130713; DOI=10.1038/35048706;
Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M.,
Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B.,
Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P.,
De Simone V., Choisne N., Artiguenave F., Robert C., Brottier P.,
Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F.,
Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V.,
Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S.,
Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G.,
Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B.,
Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G.,
Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J.,
Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D.,
Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
Monfort A., Argiriou A., Flores M., Liguori R., Vitale D.,
Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W.,
Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J.,
Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P.,
Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S.,
Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V.,
Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C.,
Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E.,
Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y.,
Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A.,
Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
Watanabe A., Yamada M., Yasuda M., Tabata S.;
"Sequence and analysis of chromosome 3 of the plant Arabidopsis
thaliana.";
Nature 408:820-822(2000).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[3]
ALTERNATIVE SPLICING, TISSUE SPECIFICITY, GENE FAMILY, AND
NOMENCLATURE.
PubMed=12954765; DOI=10.1093/nar/gkg735;
Berg A., Meza T.J., Mahic M., Thorstensen T., Kristiansen K.,
Aalen R.B.;
"Ten members of the Arabidopsis gene family encoding methyl-CpG-
binding domain proteins are transcriptionally active and at least one,
AtMBD11, is crucial for normal development.";
Nucleic Acids Res. 31:5291-5304(2003).
[4]
GENE FAMILY.
PubMed=15888682; DOI=10.1104/pp.105.060566;
Springer N.M., Kaeppler S.M.;
"Evolutionary divergence of monocot and dicot methyl-CpG-binding
domain proteins.";
Plant Physiol. 138:92-104(2005).
[5]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=16623890; DOI=10.1111/j.1365-313X.2006.02691.x;
Peng M., Cui Y., Bi Y.-M., Rothstein S.J.;
"AtMBD9: a protein with a methyl-CpG-binding domain regulates
flowering time and shoot branching in Arabidopsis.";
Plant J. 46:282-296(2006).
[6]
REVIEW.
PubMed=17208509; DOI=10.1016/j.tplants.2006.12.004;
Zemach A., Grafi G.;
"Methyl-CpG-binding domain proteins in plants: interpreters of DNA
methylation.";
Trends Plant Sci. 12:80-85(2007).
[7]
FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, AND TISSUE
SPECIFICITY.
PubMed=19419532; DOI=10.1111/j.1365-313X.2009.03860.x;
Yaish M.W.F., Peng M., Rothstein S.J.;
"AtMBD9 modulates Arabidopsis development through the dual epigenetic
pathways of DNA methylation and histone acetylation.";
Plant J. 59:123-135(2009).
-!- FUNCTION: Probable transcriptional regulator that acts as a
histone acetyltransferase. Mediates the acetylation of histone H3
and H4 of target loci (e.g. FLC). Involved in an auxin-independent
regulation of shoot branching and flowering time.
{ECO:0000269|PubMed:16623890, ECO:0000269|PubMed:19419532}.
-!- CATALYTIC ACTIVITY: Acetyl-CoA + [protein]-L-lysine = CoA +
[protein]-N(6)-acetyl-L-lysine.
-!- SUBUNIT: Interacts with histone H4.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19419532}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9SGH2-1; Sequence=Displayed;
Name=2;
IsoId=Q9SGH2-2; Sequence=Not described;
-!- TISSUE SPECIFICITY: Expressed in leaves, buds, flowers and stems.
{ECO:0000269|PubMed:12954765, ECO:0000269|PubMed:19419532}.
-!- DOMAIN: The methyl-CpG-binding domain (MBD) functions both in
binding to methylated DNA and in protein interactions.
{ECO:0000250}.
-!- DISRUPTION PHENOTYPE: Over-methylated genomic DNA. Increased shoot
branching and reduced transcription of FLC leading to early
flowering, associated with a decrease in the acetylation level in
histone H3 and H4 of FLC chromatin. {ECO:0000269|PubMed:16623890,
ECO:0000269|PubMed:19419532}.
-!- SEQUENCE CAUTION:
Sequence=AAF01531.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AC009325; AAF01531.1; ALT_SEQ; Genomic_DNA.
EMBL; AC010870; AAF24616.1; -; Genomic_DNA.
EMBL; CP002686; AEE73669.1; -; Genomic_DNA.
RefSeq; NP_186795.1; NM_111012.4. [Q9SGH2-1]
UniGene; At.41275; -.
UniGene; At.47815; -.
ProteinModelPortal; Q9SGH2; -.
SMR; Q9SGH2; -.
BioGrid; 6465; 3.
STRING; 3702.AT3G01460.1; -.
iPTMnet; Q9SGH2; -.
PaxDb; Q9SGH2; -.
PRIDE; Q9SGH2; -.
EnsemblPlants; AT3G01460.1; AT3G01460.1; AT3G01460. [Q9SGH2-1]
GeneID; 821132; -.
Gramene; AT3G01460.1; AT3G01460.1; AT3G01460.
KEGG; ath:AT3G01460; -.
Araport; AT3G01460; -.
TAIR; locus:2096672; AT3G01460.
eggNOG; ENOG410IFR9; Eukaryota.
eggNOG; ENOG41128EW; LUCA.
HOGENOM; HOG000153462; -.
InParanoid; Q9SGH2; -.
OMA; FTWPELA; -.
OrthoDB; EOG093600QJ; -.
PhylomeDB; Q9SGH2; -.
PRO; PR:Q9SGH2; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; Q9SGH2; baseline and differential.
Genevisible; Q9SGH2; AT.
GO; GO:0005720; C:nuclear heterochromatin; IBA:GO_Central.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0009506; C:plasmodesma; IDA:TAIR.
GO; GO:0004402; F:histone acetyltransferase activity; IDA:UniProtKB.
GO; GO:0042393; F:histone binding; IPI:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008327; F:methyl-CpG binding; ISS:TAIR.
GO; GO:0061630; F:ubiquitin protein ligase activity; IBA:GO_Central.
GO; GO:0016573; P:histone acetylation; IDA:UniProtKB.
GO; GO:0043966; P:histone H3 acetylation; IMP:UniProtKB.
GO; GO:0043967; P:histone H4 acetylation; IMP:UniProtKB.
GO; GO:0010216; P:maintenance of DNA methylation; IBA:GO_Central.
GO; GO:0048573; P:photoperiodism, flowering; IMP:TAIR.
GO; GO:0016567; P:protein ubiquitination; IBA:GO_Central.
GO; GO:0090308; P:regulation of methylation-dependent chromatin silencing; IBA:GO_Central.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:TAIR.
GO; GO:0010223; P:secondary shoot formation; IMP:TAIR.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 1.20.920.10; -; 1.
Gene3D; 3.30.40.10; -; 2.
InterPro; IPR036427; Bromodomain-like_sf.
InterPro; IPR016177; DNA-bd_dom_sf.
InterPro; IPR003889; FYrich_C.
InterPro; IPR003888; FYrich_N.
InterPro; IPR001739; Methyl_CpG_DNA-bd.
InterPro; IPR028942; WHIM1_dom.
InterPro; IPR028941; WHIM2_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; PF05965; FYRC; 1.
Pfam; PF05964; FYRN; 1.
Pfam; PF01429; MBD; 1.
Pfam; PF00628; PHD; 2.
Pfam; PF15612; WHIM1; 1.
Pfam; PF15613; WSD; 1.
SMART; SM00249; PHD; 2.
SUPFAM; SSF54171; SSF54171; 1.
SUPFAM; SSF57903; SSF57903; 2.
PROSITE; PS51543; FYRC; 1.
PROSITE; PS51542; FYRN; 1.
PROSITE; PS50982; MBD; 1.
PROSITE; PS01359; ZF_PHD_1; 2.
PROSITE; PS50016; ZF_PHD_2; 2.
2: Evidence at transcript level;
Alternative splicing; Bromodomain; Coiled coil; Complete proteome;
DNA-binding; Metal-binding; Nucleus; Reference proteome; Repeat;
Transcription; Transcription regulation; Transferase; Zinc;
Zinc-finger.
CHAIN 1 2176 Methyl-CpG-binding domain-containing
protein 9.
/FTId=PRO_0000405285.
DOMAIN 258 327 MBD. {ECO:0000255|PROSITE-
ProRule:PRU00338}.
DOMAIN 403 456 FYR N-terminal. {ECO:0000255|PROSITE-
ProRule:PRU00875}.
DOMAIN 550 698 FYR C-terminal. {ECO:0000255|PROSITE-
ProRule:PRU00876}.
REPEAT 1098 1137 Pumilio.
DOMAIN 1157 1228 Bromo.
ZN_FING 83 133 PHD-type 1. {ECO:0000255|PROSITE-
ProRule:PRU00146}.
ZN_FING 86 131 RING-type 1; degenerate.
ZN_FING 1287 1337 PHD-type 2. {ECO:0000255|PROSITE-
ProRule:PRU00146}.
ZN_FING 1290 1335 RING-type 2; degenerate.
COILED 491 511 {ECO:0000255}.
COILED 1251 1273 {ECO:0000255}.
COILED 1410 1437 {ECO:0000255}.
COILED 1588 1628 {ECO:0000255}.
MOTIF 914 921 Nuclear localization signal.
{ECO:0000250}.
MOTIF 1124 1131 Nuclear localization signal.
{ECO:0000250}.
MOTIF 1256 1263 Nuclear localization signal.
{ECO:0000250}.
MOTIF 1337 1344 Nuclear localization signal.
{ECO:0000250}.
MOTIF 1761 1768 Nuclear localization signal.
{ECO:0000250}.
SEQUENCE 2176 AA; 240431 MW; 05DBD955D895C3D5 CRC64;
MEPTDSTNEQ LGDTKTAAVK EESRSFLGID LNEIPTGATL GGGCTAGQDD DGEYEPVEVV
RSIHDNPDPA PGAPAEVPEP DRDASCGACG RPESIELVVV CDACERGFHM SCVNDGVEAA
PSADWMCSDC RTGGERSKLW PLGVKSKLIL DMNASPPSDA EGYGAEETSD SRKHMLASSS
CIGNSFDYAM MHSSFSSLGR GHASLEASGL MSRNTKMSMD ALGSHNLGFG FPLNLNNSSL
PMRFPSLDPS ELFLQNLRHF ISERHGVLED GWRVEFRQPL NGYQLCAVYC APNGKTFSSI
QEVACYLGLA INGNYSCMDA EIRNENSLLQ ERLHTPKRRK TSRWPNNGFP EQKGSSVSAQ
LRRFPFNGQT MSPFAVKSGT HFQAGGSLSS GNNGCGCEEA KNGCPMQFED FFVLSLGRID
IRQSYHNVNV IYPIGYKSCW HDKITGSLFT CEVSDGNSGP IFKVTRSPCS KSFIPAGSTV
FSCPKIDEMV EQNSDKLSNR RDSTQERDDD ASVEILLSEH CPPLGDDILS CLREKSFSKT
VNSLRSEVDS SRVDFDKNLS YDQDHGVEIG DIVVEEDSLS DAWKKVSQKL VDACSIVLKQ
KGTLNFLCKH VDRETSEINW DTMNEKDNVI LSLSKFCCSL APCSVTCGEK DKSEFAAVVD
ALSRWLDQNR FGLDADFVQE MIEHMPGAES CTNYRTLKSR SSSSVPITVA EGALVVKPKG
GENVKDEVFG EISRKAKKPK LNGGHGVRNL HPPPGRPMCL RLPPGLVGDF LQVSEVFWRF
HEILGFEEAF SPENLEQELI NPVFDGLFLD KPGKDDKRSE INFTDKDSTA TKLFSLFDES
RQPFPAKNTS ASELKEKKAG DSSDFKISDS SRGSCVGALL TRAHISLLQV LICELQSKVA
AFVDPNFDSG ESRSRRGRKK DDSTLSAKRN KLHMLPVNEF TWPELARRYI LSLLSMDGNL
ESAEIAARES GKVFRCLQGD GGLLCGSLTG VAGMEADSML LAEAIKKISG SLTSENDVLS
VEDDDSDGLD ATETNTCSGD IPEWAQVLEP VKKLPTNVGT RIRKCVYEAL ERNPPEWAKK
ILEHSISKEI YKGNASGPTK KAVLSLLADI RGGDLVQRSI KGTKKRTYIS VSDVIMKKCR
AVLRGVAAAD EDKVLCTLLG RKLLNSSDND DDGLLGSPAM VSRPLDFRTI DLRLAAGAYD
GSTEAFLEDV LELWSSIRVM YADQPDCVDL VATLSEKFKS LYEAEVVPLV QKLKDYRKLE
CLSAEMKKEI KDIVVSVNKL PKAPWDEGVC KVCGVDKDDD SVLLCDTCDA EYHTYCLNPP
LIRIPDGNWY CPSCVIAKRM AQEALESYKL VRRRKGRKYQ GELTRASMEL TAHLADVMEE
KDYWEFSAEE RILLLKLLCD ELLSSSLVHQ HLEQCAEAII EMQQKLRSLS SEWKNAKMRQ
EFLTAKLAKV EPSILKEVGE PHNSSYFADQ MGCDPQPQEG VGDGVTRDDE TSSTAYLNKN
QGKSPLETDT QPGESHVNFG ESKISSPETI SSPGRHELPI ADTSPLVTDN LPEKDTSETL
LKSVGRNHET HSPNSNAVEL PTAHDASSQA SQELQACQQD LSATSNEIQN LQQSIRSIES
QLLKQSIRRD FLGTDASGRL YWGCCFPDEN PRILVDGSIS LQKPVQADLI GSKVPSPFLH
TVDHGRLRLS PWTYYETETE ISELVQWLHD DDLKERDLRE SILWWKRLRY GDVQKEKKQA
QNLSAPVFAT GLETKAAMSM EKRYGPCIKL EMETLKKRGK KTKVAEREKL CRCECLESIL
PSMIHCLICH KTFASDDEFE DHTESKCIPY SLATEEGKDI SDSSKAKESL KSDYLNVKSS
AGKDVAEISN VSELDSGLIR YQEEESISPY HFEEICSKFV TKDCNRDLVK EIGLISSNGI
PTFLPSSSTH LNDSVLISAK SNKPDGGDSG DQVIFAGPET NVEGLNSESN MSFDRSVTDS
HGGPLDKPSG LGFGFSEQKN KKSSGSGLKS CCVVPQAALK RVTGKALPGF RFLKTNLLDM
DVALPEEALR PSKSHPNRRR AWRVFVKSSQ SIYELVQATI VVEDMIKTEY LKNEWWYWSS
LSAAAKISTL SALSVRIFSL DAAIIYDKPI TPSNPIDETK PIISLPDQKS QPVSDSQERS
SRVRRSGKKR KEPEGS


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