SMYD5_DANRE
ID SMYD5_DANRE Reviewed; 415 AA.
AC F1RET2; A5XCC7; Q66I88;
DT 29-SEP-2021, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2017, sequence version 3.
DT 03-AUG-2022, entry version 63.
DE RecName: Full=Histone-lysine N-trimethyltransferase SMYD5;
DE EC=2.1.1.372 {ECO:0000250|UniProtKB:Q3TYX3};
DE AltName: Full=SET and MYND domain-containing protein 5;
DE AltName: Full=[histone H4]-lysine20 N-trimethyltransferase SMYD5;
GN Name=smyd5;
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].
RC TISSUE=Ovary;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 208-360.
RX PubMed=18231586; DOI=10.1371/journal.pone.0001499;
RA Sun X.-J., Xu P.-F., Zhou T., Hu M., Fu C.-T., Zhang Y., Jin Y., Chen Y.,
RA Chen S.-J., Huang Q.-H., Liu T.X., Chen Z.;
RT "Genome-wide survey and developmental expression mapping of zebrafish SET
RT domain-containing genes.";
RL PLoS ONE 3:E1499-E1499(2008).
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, DEVELOPMENTAL STAGE, AND TISSUE
RP SPECIFICITY.
RX PubMed=27377701; DOI=10.1038/srep29157;
RA Fujii T., Tsunesumi S., Sagara H., Munakata M., Hisaki Y., Sekiya T.,
RA Furukawa Y., Sakamoto K., Watanabe S.;
RT "Smyd5 plays pivotal roles in both primitive and definitive hematopoiesis
RT during zebrafish embryogenesis.";
RL Sci. Rep. 6:29157-29157(2016).
CC -!- FUNCTION: Histone methyltransferase that specifically trimethylates
CC 'Lys-20' of histone H4 to form trimethylated histone H4 lysine 20
CC (H4K20me3) which represents a specific tag for epigenetic
CC transcriptional repression (By similarity). Plays a crucial role in
CC hematopoiesis during embryogenesis by negatively regulating expression
CC of genes related to both primitive and definitive hematopoiesis
CC (PubMed:27377701). {ECO:0000250|UniProtKB:Q3TYX3,
CC ECO:0000269|PubMed:27377701}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl(20)-[histone H4] + 3 S-adenosyl-L-methionine = 3 H(+)
CC + N(6),N(6),N(6)-trimethyl-L-lysyl(20)-[histone H4] + 3 S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:64456, Rhea:RHEA-COMP:15554, Rhea:RHEA-
CC COMP:15998, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.372;
CC Evidence={ECO:0000250|UniProtKB:Q3TYX3};
CC -!- TISSUE SPECIFICITY: Expressed at high levels in the ovary and at lower
CC levels in the fin, testis and brain. {ECO:0000269|PubMed:27377701}.
CC -!- DEVELOPMENTAL STAGE: Abundantly expressed at early developmental stages
CC but decreases slightly when embryos proceed in development
CC (PubMed:27377701). Expression is strongly detected from 0.25 to 3 hours
CC post-fertilization (hpf) in embryos, but it is only weakly observed at
CC 12 hpf (PubMed:27377701). At 24 and 36 hpf, signals are observed only
CC around the eye with stronger intensities at 24 hpf than 36 hpf
CC (PubMed:27377701). {ECO:0000269|PubMed:27377701}.
CC -!- DISRUPTION PHENOTYPE: Morpholino knockdown results in embryos which
CC show normal gross morphological development, including of heart and
CC skeletal muscle (PubMed:27377701). However, an increased expression of
CC genes related to both primitive and definitive hematopoiesis is seen
CC (PubMed:27377701). {ECO:0000269|PubMed:27377701}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
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DR EMBL; CT573285; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC081479; AAH81479.1; -; mRNA.
DR EMBL; DQ851817; ABI34488.1; -; mRNA.
DR RefSeq; NP_001004614.2; NM_001004614.2.
DR AlphaFoldDB; F1RET2; -.
DR STRING; 7955.ENSDARP00000016467; -.
DR PaxDb; F1RET2; -.
DR Ensembl; ENSDART00000021657; ENSDARP00000016467; ENSDARG00000071669.
DR GeneID; 447875; -.
DR KEGG; dre:447875; -.
DR CTD; 10322; -.
DR ZFIN; ZDB-GENE-040912-39; smyd5.
DR eggNOG; KOG2084; Eukaryota.
DR GeneTree; ENSGT00510000047420; -.
DR HOGENOM; CLU_054216_0_0_1; -.
DR OMA; LMAMYQQ; -.
DR OrthoDB; 1001347at2759; -.
DR PhylomeDB; F1RET2; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 14.
DR Bgee; ENSDARG00000071669; Expressed in tail and 22 other tissues.
DR GO; GO:0042799; F:histone methyltransferase activity (H4-K20 specific); ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0060216; P:definitive hemopoiesis; IMP:ZFIN.
DR GO; GO:0034773; P:histone H4-K20 trimethylation; ISS:UniProtKB.
DR GO; GO:0045814; P:negative regulation of gene expression, epigenetic; ISS:UniProtKB.
DR GO; GO:0045638; P:negative regulation of myeloid cell differentiation; IMP:ZFIN.
DR GO; GO:0060215; P:primitive hemopoiesis; IMP:ZFIN.
DR GO; GO:2000736; P:regulation of stem cell differentiation; ISS:UniProtKB.
DR GO; GO:2000035; P:regulation of stem cell division; ISS:UniProtKB.
DR CDD; cd10521; SET_SMYD5; 1.
DR Gene3D; 2.170.270.10; -; 1.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR044422; SMYD5_SET.
DR Pfam; PF00856; SET; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS50280; SET; 1.
PE 2: Evidence at transcript level;
KW Metal-binding; Methyltransferase; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..415
FT /note="Histone-lysine N-trimethyltransferase SMYD5"
FT /id="PRO_0000453202"
FT DOMAIN 20..351
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT ZN_FING 95..135
FT /note="MYND-type"
FT REGION 388..415
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 350
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT CONFLICT 327
FT /note="E -> D (in Ref. 2; AAH81479 and 3; ABI34488)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 415 AA; 47175 MW; 0DB85DB1C9E6CD2B CRC64;
MAAPVDDMFS RCVDSAKASN CVDVRFINNV KGKGLFAKKP FKKGDTIFIE RPLVSSQFLW
NALYKYRACE YCLRALETAE ENARRLSGLP ALILPHPELC KVRPDRHQAC PQCQVMYCSS
ECRQAAMDQY HKILCLGPSN DDPDHPVNKL QDAWRSVHFP PETSSVMILA KMVATIKQTQ
DKERWQRLFT NFCSRTANEE EEIVHKLLGE KFQGQLGLLR NLFTTALYED RLSQWFTPEG
FRSLFSLVGT NGQGIGTSSL SQWVHACDAL ELPRQQREQL DAFIDQLYKD IDKETGDFLN
CEGSGLFLLQ SSCNHSCVPN AEASFPENNF LLHLTALGDI GPGEEICISY LDCCQRDRSR
HSRHKILREN YLFICSCQKC LSQMDDADMT SEDEEEVEGE GETEGEDMED EMTDV
