SUVR4_ARATH
ID SUVR4_ARATH Reviewed; 492 AA.
AC Q8W595; Q3EBC4; Q9M848;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 02-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Histone-lysine N-methyltransferase SUVR4;
DE EC=2.1.1.- {ECO:0000269|PubMed:21423664};
DE EC=2.1.1.366 {ECO:0000269|PubMed:21423664};
DE AltName: Full=Protein SET DOMAIN GROUP 31;
DE AltName: Full=Suppressor of variegation 3-9-related protein 4;
DE Short=Su(var)3-9-related protein 4;
GN Name=SUVR4; Synonyms=SDG31, SET31; OrderedLocusNames=At3g04380;
GN ORFNames=T27C4.2;
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 [MRNA], 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).
RN [2]
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 [3]
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 [4]
RP FUNCTION, INTERACTION WITH UBIQUITIN, AND CATALYTIC ACTIVITY.
RX PubMed=21423664; DOI=10.1371/journal.pgen.1001325;
RA Veiseth S.V., Rahman M.A., Yap K.L., Fischer A., Egge-Jacobsen W.,
RA Reuter G., Zhou M.M., Aalen R.B., Thorstensen T.;
RT "The SUVR4 histone lysine methyltransferase binds ubiquitin and converts
RT H3K9me1 to H3K9me3 on transposon chromatin in Arabidopsis.";
RL PLoS Genet. 7:E1001325-E1001325(2011).
RN [5]
RP STRUCTURE BY NMR OF 1-89, AND INTERACTION WITH UBIQUITIN.
RX PubMed=24625295; DOI=10.1021/bi401436h;
RA Rahman M.A., Kristiansen P.E., Veiseth S.V., Andersen J.T., Yap K.L.,
RA Zhou M.M., Sandlie I., Thorstensen T., Aalen R.B.;
RT "The Arabidopsis histone methyltransferase SUVR4 binds ubiquitin via a
RT domain with a four-helix bundle structure.";
RL Biochemistry 53:2091-2100(2014).
CC -!- FUNCTION: Histone methyltransferase that converts monomethylated 'Lys-
CC 9' of histone H3 (H3K9me1) to dimethylated 'Lys-9' (H3K9me2) in the
CC absence of bound ubiquitin, and to trimethylated 'Lys-9' (H3K9me3) in
CC the presence of bound ubiquitin. Acts in a locus-specific manner and
CC contributes to the transcriptional silencing of pseudogenes and
CC transposons. H3 'Lys-9' methylation represents a specific tag for
CC epigenetic transcriptional repression. {ECO:0000269|PubMed:21423664}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=N(6)-methyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine
CC = H(+) + N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:60284, Rhea:RHEA-COMP:15541, Rhea:RHEA-
CC COMP:15542, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:61929, ChEBI:CHEBI:61976; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00913, ECO:0000269|PubMed:21423664};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-
CC methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3]
CC + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60288, Rhea:RHEA-
CC COMP:15538, Rhea:RHEA-COMP:15541, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961,
CC ChEBI:CHEBI:61976; EC=2.1.1.366; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00913, ECO:0000269|PubMed:21423664};
CC -!- SUBUNIT: Interacts with ubiquitin. {ECO:0000269|PubMed:21423664,
CC ECO:0000269|PubMed:24625295}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Chromosome {ECO:0000250}.
CC Note=Associates with euchromatic regions. {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=Q8W595-1; Sequence=Displayed;
CC -!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that are
CC arranged in a triangular cluster; some of these Cys residues contribute
CC to the binding of two zinc ions within the cluster. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Histone-lysine methyltransferase family.
CC {ECO:0000255|PROSITE-ProRule:PRU00913}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF63769.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF408062; AAL01113.2; -; mRNA.
DR EMBL; AC022287; AAF63769.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE74073.1; -; Genomic_DNA.
DR RefSeq; NP_187088.2; NM_111309.3. [Q8W595-1]
DR PDB; 2LXE; NMR; -; A=1-89.
DR PDBsum; 2LXE; -.
DR AlphaFoldDB; Q8W595; -.
DR BMRB; Q8W595; -.
DR SMR; Q8W595; -.
DR BioGRID; 4928; 6.
DR IntAct; Q8W595; 3.
DR STRING; 3702.AT3G04380.1; -.
DR PaxDb; Q8W595; -.
DR PRIDE; Q8W595; -.
DR ProteomicsDB; 226530; -. [Q8W595-1]
DR EnsemblPlants; AT3G04380.1; AT3G04380.1; AT3G04380. [Q8W595-1]
DR GeneID; 819593; -.
DR Gramene; AT3G04380.1; AT3G04380.1; AT3G04380. [Q8W595-1]
DR KEGG; ath:AT3G04380; -.
DR Araport; AT3G04380; -.
DR TAIR; locus:2100885; AT3G04380.
DR eggNOG; KOG1082; Eukaryota.
DR InParanoid; Q8W595; -.
DR OrthoDB; 260204at2759; -.
DR PhylomeDB; Q8W595; -.
DR BRENDA; 2.1.1.B130; 399.
DR PRO; PR:Q8W595; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8W595; baseline and differential.
DR GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IDA:TAIR.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0034968; P:histone lysine methylation; IDA:UniProtKB.
DR Gene3D; 1.10.8.850; -; 1.
DR Gene3D; 2.170.270.10; -; 1.
DR InterPro; IPR007728; Pre-SET_dom.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR025776; SUVR4/1/2.
DR InterPro; IPR043017; WIYLD_dom_sf.
DR InterPro; IPR018848; WIYLD_domain.
DR Pfam; PF05033; Pre-SET; 1.
DR Pfam; PF00856; SET; 1.
DR Pfam; PF10440; WIYLD; 1.
DR SMART; SM00468; PreSET; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS50867; PRE_SET; 1.
DR PROSITE; PS51580; SAM_MT43_3; 1.
DR PROSITE; PS50280; SET; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Chromatin regulator; Chromosome;
KW Metal-binding; Methyltransferase; Nucleus; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; Zinc.
FT CHAIN 1..492
FT /note="Histone-lysine N-methyltransferase SUVR4"
FT /id="PRO_0000233368"
FT DOMAIN 196..299
FT /note="Pre-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00157"
FT DOMAIN 302..435
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT DOMAIN 446..462
FT /note="Post-SET"
FT REGION 112..138
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 463..492
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 112..131
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 463..484
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 196
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 196
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 197
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 200
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 200
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 204
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 213
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 281
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 281
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 285
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 287
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 291
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 313..315
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 391..392
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 394
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 434
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 450
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 452
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT BINDING 457
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q9H5I1"
FT CONFLICT 302
FT /note="C -> W (in Ref. 1; AAL01113)"
FT /evidence="ECO:0000305"
FT CONFLICT 482..488
FT /note="QGSKEVS -> ARFQRGV (in Ref. 1; AAL01113)"
FT /evidence="ECO:0000305"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:2LXE"
FT TURN 14..16
FT /evidence="ECO:0007829|PDB:2LXE"
FT HELIX 17..21
FT /evidence="ECO:0007829|PDB:2LXE"
FT HELIX 29..38
FT /evidence="ECO:0007829|PDB:2LXE"
FT HELIX 43..56
FT /evidence="ECO:0007829|PDB:2LXE"
FT HELIX 61..64
FT /evidence="ECO:0007829|PDB:2LXE"
FT TURN 65..68
FT /evidence="ECO:0007829|PDB:2LXE"
FT HELIX 70..80
FT /evidence="ECO:0007829|PDB:2LXE"
SQ SEQUENCE 492 AA; 55855 MW; 86DA23CF75DD158E CRC64;
MISLSGLTSS VESDLDMQQA MLTNKDEKVL KALERTRQLD IPDEKTMPVL MKLLEEAGGN
WSYIKLDNYT ALVDAIYSVE DENKQSEGSS NGNRGKNLKV IDSPATLKKT YETRSASSGS
SIQVVQKQPQ LSNGDRKRKY KSRIADITKG SESVKIPLVD DVGSEAVPKF TYIPHNIVYQ
SAYLHVSLAR ISDEDCCANC KGNCLSADFP CTCARETSGE YAYTKEGLLK EKFLDTCLKM
KKEPDSFPKV YCKDCPLERD HDKGTYGKCD GHLIRKFIKE CWRKCGCDMQ CGNRVVQRGI
RCQLQVYFTQ EGKGWGLRTL QDLPKGTFIC EYIGEILTNT ELYDRNVRSS SERHTYPVTL
DADWGSEKDL KDEEALCLDA TICGNVARFI NHRCEDANMI DIPIEIETPD RHYYHIAFFT
LRDVKAMDEL TWDYMIDFND KSHPVKAFRC CCGSESCRDR KIKGSQGKSI ERRKIVSAKK
QQGSKEVSKK RK
