SMY2B_DANRE
ID SMY2B_DANRE Reviewed; 434 AA.
AC Q5RGL7; Q1JPT4;
DT 08-MAR-2011, integrated into UniProtKB/Swiss-Prot.
DT 08-MAR-2011, sequence version 2.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=N-lysine methyltransferase SMYD2-B;
DE EC=2.1.1.- {ECO:0000250|UniProtKB:Q9NRG4};
DE AltName: Full=Histone methyltransferase SMYD2-B;
DE EC=2.1.1.354 {ECO:0000269|PubMed:16477022};
DE AltName: Full=SET and MYND domain-containing protein 2B;
GN Name=smyd2b; ORFNames=si:dkey-121j17.3;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=16477022; DOI=10.1073/pnas.0509503103;
RA Tan X., Rotllant J., Li H., De Deyne P., DeDeyne P., Du S.J.;
RT "SmyD1, a histone methyltransferase, is required for myofibril organization
RT and muscle contraction in zebrafish embryos.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:2713-2718(2006).
CC -!- FUNCTION: Protein-lysine N-methyltransferase that methylates both
CC histones and non-histone proteins, including p53/TP53 and RB1.
CC Specifically trimethylates histone H3 'Lys-4' (H3K4me3) in vivo. The
CC activity requires interaction with HSP90alpha. Shows even higher
CC methyltransferase activity on p53/TP53. Monomethylates 'Lys-370' of
CC p53/TP53, leading to decreased DNA-binding activity and subsequent
CC transcriptional regulation activity of p53/TP53. Monomethylates RB1 at
CC 'Lys-860'. {ECO:0000250|UniProtKB:Q9NRG4}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) +
CC N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:60260, Rhea:RHEA-COMP:15537, Rhea:RHEA-
CC COMP:15547, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.354;
CC Evidence={ECO:0000269|PubMed:16477022};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl-[protein] + S-adenosyl-L-methionine = H(+) + N(6)-
CC methyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:51736, Rhea:RHEA-COMP:9752, Rhea:RHEA-COMP:13053,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61929;
CC Evidence={ECO:0000250|UniProtKB:Q9NRG4};
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000250}. Nucleus
CC {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q5RGL7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q5RGL7-2; Sequence=VSP_040727;
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAI20605.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; BX855610; CAI20605.1; ALT_SEQ; Genomic_DNA.
DR EMBL; BC116606; AAI16607.1; -; mRNA.
DR RefSeq; NP_001038756.1; NM_001045291.1. [Q5RGL7-2]
DR RefSeq; XP_005164480.1; XM_005164423.3. [Q5RGL7-1]
DR AlphaFoldDB; Q5RGL7; -.
DR SMR; Q5RGL7; -.
DR STRING; 7955.ENSDARP00000005268; -.
DR PaxDb; Q5RGL7; -.
DR PRIDE; Q5RGL7; -.
DR Ensembl; ENSDART00000031759; ENSDARP00000036459; ENSDARG00000005629. [Q5RGL7-2]
DR Ensembl; ENSDART00000162198; ENSDARP00000133013; ENSDARG00000005629. [Q5RGL7-1]
DR GeneID; 568616; -.
DR KEGG; dre:568616; -.
DR CTD; 568616; -.
DR ZFIN; ZDB-GENE-041001-201; smyd2b.
DR eggNOG; KOG2084; Eukaryota.
DR GeneTree; ENSGT00940000166832; -.
DR HOGENOM; CLU_018406_0_0_1; -.
DR InParanoid; Q5RGL7; -.
DR PhylomeDB; Q5RGL7; -.
DR TreeFam; TF106487; -.
DR PRO; PR:Q5RGL7; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 20.
DR Bgee; ENSDARG00000005629; Expressed in muscle tissue and 11 other tissues.
DR ExpressionAtlas; Q5RGL7; baseline.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005829; C:cytosol; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0046975; F:histone methyltransferase activity (H3-K36 specific); ISS:UniProtKB.
DR GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016279; F:protein-lysine N-methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0000993; F:RNA polymerase II complex binding; ISS:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0060047; P:heart contraction; IGI:ZFIN.
DR GO; GO:0007507; P:heart development; IGI:ZFIN.
DR GO; GO:0034968; P:histone lysine methylation; IBA:GO_Central.
DR GO; GO:0008285; P:negative regulation of cell population proliferation; ISS:UniProtKB.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; ISS:UniProtKB.
DR GO; GO:0018027; P:peptidyl-lysine dimethylation; ISS:UniProtKB.
DR GO; GO:0018026; P:peptidyl-lysine monomethylation; ISS:UniProtKB.
DR GO; GO:0043516; P:regulation of DNA damage response, signal transduction by p53 class mediator; ISS:UniProtKB.
DR Gene3D; 1.25.40.10; -; 1.
DR Gene3D; 2.170.270.10; -; 1.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR InterPro; IPR002893; Znf_MYND.
DR Pfam; PF00856; SET; 1.
DR Pfam; PF01753; zf-MYND; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS50280; SET; 1.
DR PROSITE; PS01360; ZF_MYND_1; 1.
DR PROSITE; PS50865; ZF_MYND_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chromatin regulator; Cytoplasm; Metal-binding;
KW Methyltransferase; Nucleus; Reference proteome; S-adenosyl-L-methionine;
KW Transcription; Transcription regulation; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..434
FT /note="N-lysine methyltransferase SMYD2-B"
FT /id="PRO_0000405849"
FT DOMAIN 8..242
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT ZN_FING 53..91
FT /note="MYND-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 18..20
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 53
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 56
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 69
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 75
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 79
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 87
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 91
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 138
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 207..208
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 259..261
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT VAR_SEQ 107..117
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.2"
FT /id="VSP_040727"
SQ SEQUENCE 434 AA; 49630 MW; EB9BB6A77675D2BA CRC64;
MMKAEGIPGI EQFASPGKGR GLRVSRAYGV GELLFSCPAY SYVLSVGERG LICEQCFTRK
KGLAKCGKCK KAFYCNANCQ KKNWPMHKLE CQAMCAFGEN WRPSETVRLV ARIIARLKAQ
KERSPSEILL LLGEMEAHLE DMDNEKREMT EAHIAGLHQF YSKHLDFPDH QALLTLFSQV
HCNGFTVEDE ELSNLGLAIF PDIALLNHSC SPNVIVTYRG INAEVRAVKD ISPGQEIYTS
YIDLLYPTAD RLERLRDMYY FSCDCKECTT KSMDVVKMSV RKRSDEIGEK EIKDMVRYAR
NSMENFRRAK QDKSPTELLE MCELSIDKMS TVFDDSNVYI LHMMYQAMGI CLFTEDYEGA
VRYGEKVIKP FTVLYPAYSM NVASMFLKLG RLYIALDRKL AGIDAFQKAL TIMEVVHGKD
HTYVTELKQE MRDF
