ATX4_ARATH
ID ATX4_ARATH Reviewed; 1027 AA.
AC Q9SUE7; Q941H0;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 24-MAR-2009, sequence version 3.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=Histone-lysine N-methyltransferase ATX4;
DE EC=2.1.1.-;
DE AltName: Full=Protein SET DOMAIN GROUP 16;
DE AltName: Full=Trithorax-homolog protein 4;
DE Short=TRX-homolog protein 4;
DE Short=Trithorax 4;
GN Name=ATX4; Synonyms=SDG16, SET16, TX4; OrderedLocusNames=At4g27910;
GN ORFNames=T13J8.20;
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 [MRNA] OF 743-1027, AND 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 -!- 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=CAB36760.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB79593.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL035524; CAB36760.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161572; CAB79593.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE85408.1; -; Genomic_DNA.
DR EMBL; AY049754; AAL12215.1; -; mRNA.
DR PIR; T02892; T02892.
DR RefSeq; NP_194520.3; NM_118929.5.
DR AlphaFoldDB; Q9SUE7; -.
DR SMR; Q9SUE7; -.
DR STRING; 3702.AT4G27910.1; -.
DR iPTMnet; Q9SUE7; -.
DR PaxDb; Q9SUE7; -.
DR PRIDE; Q9SUE7; -.
DR ProteomicsDB; 240921; -.
DR EnsemblPlants; AT4G27910.1; AT4G27910.1; AT4G27910.
DR GeneID; 828904; -.
DR Gramene; AT4G27910.1; AT4G27910.1; AT4G27910.
DR KEGG; ath:AT4G27910; -.
DR Araport; AT4G27910; -.
DR TAIR; locus:2132912; AT4G27910.
DR eggNOG; KOG1080; Eukaryota.
DR HOGENOM; CLU_006335_0_0_1; -.
DR InParanoid; Q9SUE7; -.
DR OMA; WIQETAV; -.
DR OrthoDB; 112057at2759; -.
DR PhylomeDB; Q9SUE7; -.
DR PRO; PR:Q9SUE7; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SUE7; baseline and differential.
DR Genevisible; Q9SUE7; AT.
DR GO; GO:0031011; C:Ino80 complex; IDA:TAIR.
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; 3.30.40.10; -; 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; 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; 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; 1.
DR PROSITE; PS50016; ZF_PHD_2; 2.
PE 2: Evidence at transcript level;
KW Chromatin regulator; Metal-binding; Methyltransferase; Nucleus;
KW Reference proteome; Repeat; S-adenosyl-L-methionine; Transferase; Zinc;
KW Zinc-finger.
FT CHAIN 1..1027
FT /note="Histone-lysine N-methyltransferase ATX4"
FT /id="PRO_0000233357"
FT DOMAIN 207..276
FT /note="PWWP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00162"
FT DOMAIN 885..1002
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT DOMAIN 1011..1027
FT /note="Post-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT ZN_FING 646..680
FT /note="C2HC pre-PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT ZN_FING 704..761
FT /note="PHD-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT REGION 75..104
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 895
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 939
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 962..963
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 965
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1015
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1017
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1022
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT CONFLICT 787
FT /note="K -> E (in Ref. 3; AAL12215)"
FT /evidence="ECO:0000305"
FT CONFLICT 851..853
FT /note="AAI -> TAV (in Ref. 3; AAL12215)"
FT /evidence="ECO:0000305"
FT CONFLICT 901
FT /note="A -> G (in Ref. 3; AAL12215)"
FT /evidence="ECO:0000305"
FT CONFLICT 947
FT /note="V -> L (in Ref. 3; AAL12215)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1027 AA; 116739 MW; 925666F8ADEFC0B4 CRC64;
MIIKRKFKTQ IPSLERCKLG NESRKKKRKL NLGGGGYYYP LNLLGEIAAG IVPGNGRNGF
SASWCTEVTK PVEVEESLSK RRSDSGTVRD SPPAEVSRPP LVRTSRGRIQ VLPSRFNDSV
LDNWRKDSKS DCDLEEEEIE CRNEKVVSFR VPKATNLKSK ELDRKSKYSA LCKEERFHEQ
HNDEARARVD EKLPNKKGTF GPENFYSGDL VWAKSGRNEP FWPAIVIDPM TQAPELVLRS
CIPDAACVVF FGHSGNENER DYAWVRRGMI FPFVDYVARF QEQPELQGCK PGNFQMALEE
AFLADQGFTE KLMHDIHLAA GNSTFDDSFY RWIQETAVSN QELNNNAPRQ GLLKKHRNPL
ACAGCETVIS FEMAKKMKDL IPGDQLLCKP CSRLTKSKHI CGICKKIRNH LDNKSWVRCD
GCKVRIHAEC DQISDRHLKD LRETDYYCPT CRAKFNFDLS DSEKQNSKSK VAKGDGQMVL
PDKVIVVCAG VEGVYFPRLH LVVCKCGSCG PKKKALSEWE RHTGSKSKNW KTSVKVKSSK
LALEDWMMNL AELHANATAA KVPKRPSIKQ RKQRLLAFLS ETYEPVNAKW TTERCAVCRW
VEDWDYNKII ICNRCQIAVH QECYGARHVR DFTSWVCKAC ERPDIKRECC LCPVKGGALK
PTDVETLWVH VTCAWFQPEV CFASEEKMEP AVGILSIPST NFVKICVICK QIHGSCTQCC
KCSTYYHAMC ASRAGYRMEL HCLEKNGQQI TKMVSYCAYH RAPNPDNVLI IQTPSGAFSA
KSLVQNKKKG GSRLISLIRE DDEAPAENTI TCDPFSAARC RVFKRKINSK KRIEEEAIPH
HTRGPRHHAS AAIQTLNTFR HVPEEPKSFS SFRERLHHLQ RTEMDRVCFG RSGIHGWGLF
ARRNIQEGEM VLEYRGEQVR GSIADLREAR YRRVGKDCYL FKISEEVVVD ATDKGNIARL
INHSCTPNCY ARIMSVGDEE SRIVLIAKAN VAVGEELTYD YLFDPDEAEE LKVPCLCKAP
NCRKFMN
