ATX3_ARATH
ID ATX3_ARATH Reviewed; 1018 AA.
AC Q9M364; C0SVF7; Q0WU37;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 22-SEP-2009, sequence version 2.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Histone-lysine N-methyltransferase ATX3;
DE EC=2.1.1.-;
DE AltName: Full=Protein SET DOMAIN GROUP 14;
DE AltName: Full=Trithorax-homolog protein 3;
DE Short=TRX-homolog protein 3;
GN Name=ATX3; Synonyms=SDG14, SET14; OrderedLocusNames=At3g61740;
GN ORFNames=F15G16.130;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Fujita M., Mizukado S., Seki M., Shinozaki K., Mitsuda N., Takiguchi Y.,
RA Takagi M.;
RT "ORF cloning and analysis of Arabidopsis transcription factor genes.";
RL Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NOMENCLATURE.
RX PubMed=11691919; DOI=10.1093/nar/29.21.4319;
RA Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K.,
RA Assalkhou R., Schulz I., Reuter G., Aalen R.B.;
RT "The Arabidopsis thaliana genome contains at least 29 active genes encoding
RT SET domain proteins that can be assigned to four evolutionarily conserved
RT classes.";
RL Nucleic Acids Res. 29:4319-4333(2001).
CC -!- FUNCTION: Histone methyltransferase. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) + N(6)-
CC methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61929;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9M364-1; Sequence=Displayed;
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Histone-lysine methyltransferase family. TRX/MLL
CC subfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB71104.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL132959; CAB71104.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE80250.1; -; Genomic_DNA.
DR EMBL; AK227351; BAE99361.1; -; mRNA.
DR EMBL; AB493660; BAH30498.1; -; mRNA.
DR PIR; T47966; T47966.
DR RefSeq; NP_191733.3; NM_116039.4. [Q9M364-1]
DR AlphaFoldDB; Q9M364; -.
DR SMR; Q9M364; -.
DR BioGRID; 10661; 3.
DR STRING; 3702.AT3G61740.1; -.
DR PaxDb; Q9M364; -.
DR PRIDE; Q9M364; -.
DR EnsemblPlants; AT3G61740.1; AT3G61740.1; AT3G61740. [Q9M364-1]
DR GeneID; 825347; -.
DR Gramene; AT3G61740.1; AT3G61740.1; AT3G61740. [Q9M364-1]
DR KEGG; ath:AT3G61740; -.
DR Araport; AT3G61740; -.
DR TAIR; locus:2076755; AT3G61740.
DR eggNOG; KOG1080; Eukaryota.
DR InParanoid; Q9M364; -.
DR OrthoDB; 112057at2759; -.
DR PhylomeDB; Q9M364; -.
DR PRO; PR:Q9M364; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9M364; baseline and differential.
DR Genevisible; Q9M364; AT.
DR GO; GO:0048188; C:Set1C/COMPASS complex; IDA:TAIR.
DR GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0051571; P:positive regulation of histone H3-K4 methylation; IGI:TAIR.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR CDD; cd15663; ePHD_ATX3_4_5_like; 1.
DR CDD; cd15495; PHD_ATX3_4_5_like; 1.
DR Gene3D; 2.170.270.10; -; 1.
DR Gene3D; 3.10.390.10; -; 1.
DR Gene3D; 3.30.40.10; -; 3.
DR InterPro; IPR041955; ATX3/4/5_ePHD.
DR InterPro; IPR042011; ATX3/4/5_PHD.
DR InterPro; IPR034732; EPHD.
DR InterPro; IPR025780; Hist-Lys_N-MeTrfase_ATX.
DR InterPro; IPR003616; Post-SET_dom.
DR InterPro; IPR000313; PWWP_dom.
DR InterPro; IPR010919; SAND-like_dom_sf.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF00628; PHD; 1.
DR Pfam; PF00855; PWWP; 1.
DR Pfam; PF00856; SET; 1.
DR SMART; SM00249; PHD; 3.
DR SMART; SM00508; PostSET; 1.
DR SMART; SM00293; PWWP; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF57903; SSF57903; 2.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS51805; EPHD; 1.
DR PROSITE; PS50868; POST_SET; 1.
DR PROSITE; PS50812; PWWP; 1.
DR PROSITE; PS51566; SAM_MT43_TRX_MLL; 1.
DR PROSITE; PS50280; SET; 1.
DR PROSITE; PS01359; ZF_PHD_1; 2.
DR PROSITE; PS50016; ZF_PHD_2; 2.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chromatin regulator; Metal-binding;
KW Methyltransferase; Nucleus; Reference proteome; Repeat;
KW S-adenosyl-L-methionine; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..1018
FT /note="Histone-lysine N-methyltransferase ATX3"
FT /id="PRO_0000233356"
FT DOMAIN 189..258
FT /note="PWWP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00162"
FT DOMAIN 875..993
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT DOMAIN 1002..1018
FT /note="Post-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT ZN_FING 600..634
FT /note="C2HC pre-PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT ZN_FING 658..715
FT /note="PHD-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT REGION 39..150
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 50..82
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 96..121
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 130..150
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 885
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 929
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 952..953
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 955
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1006
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1008
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1013
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT CONFLICT 87
FT /note="P -> S (in Ref. 3; BAE99361)"
FT /evidence="ECO:0000305"
FT CONFLICT 1000
FT /note="E -> G (in Ref. 3; BAE99361)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1018 AA; 115689 MW; DC6D1992C4AA66D2 CRC64;
MILKRTLTTF ENQNLKRCKI DSEIEYGRKK GEIIVYKKRQ RATVDQPCSK EPELLTSSSS
SLTSKEESQQ VCSDQSKSSR GRVRAVPSRF KDSIVGTWKS SRRKGESTES SHDDDDVSLG
KKVKGFSGSS KLHRSKDSKV FPRKDNGDSS EVDCDYWDVQ ISYDDANFGM PKKSDASRKG
VYKPEEFTVG DLVWAKCGKR FPAWPAVVID PISQAPDGVL KHCVPGAICV MFFGYSKDGT
QRDYAWVRQG MVYPFTEFMD KFQDQTNLFN YKASEFNKAL EEAVLAENGN FGDAEIISPD
SSATESDQDY GPASRFQGSY HEDIRTCDGC GSVMPLKSLK RTKDSQPEEL LCKHCSKLRK
SNQYCGICKR IWHPSDDGDW VCCDGCDVWV HAECDNITNE RFKELEHNNY YCPDCKVQHE
LTPTILEEQN SVFKSTEKTT ETGLPDAITV VCNGMEGTYI RKFHAIECKC GSCGSRKQSP
SEWERHTGCR AKKWKYSVRV KDTMLPLEKW IAEFSTYTLE TQMLDKQKML SLLEEKYEPV
RAKWTTERCA VCRWVEDWEE NKMIICNRCQ VAVHQECYGV SKSQDLTSWV CRACETPDIE
RDCCLCPVKG GALKPSDVEG LWVHVTCAWF RPEVGFLNHE NMEPAVGLFK IPANSFLKVC
TICKQTHGSC VHCCKCATHF HAMCASRAGY NMELHCLEKN GVQRTRKSVY CSFHRKPDPD
SVVVVHTPSG VFGSRNLLQN QYGRAKGSRL VLTKKMKLPG FQTQTQAEQS RVFDSLSAAR
CRIYSRSNTK IDLEAISHRL KGPSHHSLSA IENLNSFKAS FSFRAPFMSV FCFLGATFSE
YLRKILISIY LVTHQEADFT SFRERLKHLQ RTENFRVCFG KSGIHGWGLF ARKSIQEGEM
IIEYRGVKVR RSVADLREAN YRSQGKDCYL FKISEEIVID ATDSGNIARL INHSCMPNCY
ARIVSMGDGE DNRIVLIAKT NVAAGEELTY DYLFEVDESE EIKVPCLCKA PNCRKFMN
