STB1B_DANRE
ID STB1B_DANRE Reviewed; 1216 AA.
AC Q08BR4; Q06ZW4;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 03-APR-2007, sequence version 2.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=Histone-lysine N-methyltransferase SETDB1-B;
DE EC=2.1.1.354 {ECO:0000250|UniProtKB:Q15047};
DE AltName: Full=SET domain bifurcated 1B;
GN Name=setdb1b; ORFNames=zgc:152899;
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 MRNA] OF 1-1204.
RC STRAIN=AB;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 373-1216.
RC TISSUE=Kidney marrow;
RX PubMed=15520368; DOI=10.1073/pnas.0407241101;
RA Song H.-D., Sun X.-J., Deng M., Zhang G.-W., Zhou Y., Wu X.-Y., Sheng Y.,
RA Chen Y., Ruan Z., Jiang C.-L., Fan H.-Y., Zon L.I., Kanki J.P., Liu T.X.,
RA Look A.T., Chen Z.;
RT "Hematopoietic gene expression profile in zebrafish kidney marrow.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:16240-16245(2004).
CC -!- FUNCTION: Histone methyltransferase that specifically trimethylates
CC 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific
CC tag for epigenetic transcriptional repression by recruiting HP1 (CBX1,
CC CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in
CC euchromatin regions, thereby playing a central role in the silencing of
CC euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA
CC methylation. Plays a role in promoter hypermethylation and
CC transcriptional silencing of tumor suppressor genes (TSGs) or other
CC tumor-related genes. Also required to maintain a transcriptionally
CC repressive state of genes in undifferentiated embryonic stem cells
CC (ESCs). Associates at promoter regions of tumor suppressor genes (TSGs)
CC leading to their gene silencing (By similarity).
CC {ECO:0000250|UniProtKB:Q15047}.
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:0000250|UniProtKB:Q15047, ECO:0000255|PROSITE-
CC ProRule:PRU00906};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Chromosome {ECO:0000250}.
CC Note=Associated with non-pericentromeric regions of chromatin. Excluded
CC from nucleoli and islands of condensed chromatin (By similarity).
CC {ECO:0000250}.
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. Suvar3-9
CC subfamily. {ECO:0000255|PROSITE-ProRule:PRU00906}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAI24602.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; BC124601; AAI24602.1; ALT_FRAME; mRNA.
DR EMBL; DQ358103; ABC88478.1; -; mRNA.
DR AlphaFoldDB; Q08BR4; -.
DR SMR; Q08BR4; -.
DR STRING; 7955.ENSDARP00000082796; -.
DR PaxDb; Q08BR4; -.
DR PRIDE; Q08BR4; -.
DR ZFIN; ZDB-GENE-061013-224; setdb1b.
DR eggNOG; KOG1141; Eukaryota.
DR InParanoid; Q08BR4; -.
DR PhylomeDB; Q08BR4; -.
DR Reactome; R-DRE-3214841; PKMTs methylate histone lysines.
DR PRO; PR:Q08BR4; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0046974; F:histone methyltransferase activity (H3-K9 specific); IBA:GO_Central.
DR GO; GO:1990841; F:promoter-specific chromatin binding; ISS:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0070828; P:heterochromatin organization; IBA:GO_Central.
DR GO; GO:0051567; P:histone H3-K9 methylation; IBA:GO_Central.
DR GO; GO:0010629; P:negative regulation of gene expression; IBA:GO_Central.
DR GO; GO:0090309; P:positive regulation of DNA methylation-dependent heterochromatin assembly; ISS:UniProtKB.
DR GO; GO:0007265; P:Ras protein signal transduction; ISS:UniProtKB.
DR Gene3D; 2.170.270.10; -; 2.
DR InterPro; IPR016177; DNA-bd_dom_sf.
DR InterPro; IPR040880; DUF5604.
DR InterPro; IPR025796; Hist-Lys_N-MeTrfase_SETDB1.
DR InterPro; IPR001739; Methyl_CpG_DNA-bd.
DR InterPro; IPR003616; Post-SET_dom.
DR InterPro; IPR007728; Pre-SET_dom.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR002999; Tudor.
DR InterPro; IPR041292; Tudor_4.
DR InterPro; IPR041291; TUDOR_5.
DR Pfam; PF18300; DUF5604; 1.
DR Pfam; PF01429; MBD; 1.
DR Pfam; PF05033; Pre-SET; 1.
DR Pfam; PF00856; SET; 1.
DR Pfam; PF18358; Tudor_4; 1.
DR Pfam; PF18359; Tudor_5; 1.
DR SMART; SM00391; MBD; 1.
DR SMART; SM00468; PreSET; 1.
DR SMART; SM00317; SET; 1.
DR SMART; SM00333; TUDOR; 2.
DR SUPFAM; SSF54171; SSF54171; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS50868; POST_SET; 1.
DR PROSITE; PS50867; PRE_SET; 1.
DR PROSITE; PS51573; SAM_MT43_SUVAR39_1; 1.
DR PROSITE; PS50280; SET; 1.
PE 2: Evidence at transcript level;
KW Chromatin regulator; Chromosome; Coiled coil; Metal-binding;
KW Methyltransferase; Nucleus; Reference proteome; Repeat; Repressor;
KW S-adenosyl-L-methionine; Transcription; Transcription regulation;
KW Transferase; Zinc.
FT CHAIN 1..1216
FT /note="Histone-lysine N-methyltransferase SETDB1-B"
FT /id="PRO_0000281820"
FT DOMAIN 266..329
FT /note="Tudor 1"
FT DOMAIN 356..412
FT /note="Tudor 2"
FT DOMAIN 595..666
FT /note="MBD"
FT DOMAIN 728..801
FT /note="Pre-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00157"
FT DOMAIN 804..1179
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT DOMAIN 1188..1204
FT /note="Post-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT REGION 417..513
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 892..944
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 961..1057
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1081..1108
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 38..61
FT /evidence="ECO:0000255"
FT COMPBIAS 441..460
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 465..479
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 480..504
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 898..920
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 921..940
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 962..994
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 999..1018
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1043..1057
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 730
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 730
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 732
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 736
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 736
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 742
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 744
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 782
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 782
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 786
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 788
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 793
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 814..816
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 852
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 854
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 1133
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 1136..1137
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 1139
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 1192
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 1194
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 1199
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1216 AA; 135811 MW; 44C38E80B5941AAD CRC64;
MEMELEPELE EELGVSLDEL RKWIEEQVDS SEAVQKRKAD LEQLQEWVEQ REKEVADIDA
LCSNASESVV QCEALVKEVY SNMGLVYRES SSDDEGGKAN PSEVIEIDDD DDDDVIAVGC
LVPPKKSLTQ AKDPALKEAS AALQRTSQQV QNLAQTVNRT AQSGVTTPVK TGGPPGQGPL
AVPAVFMSSA PRNTPTQPNP NIKQDSIKIN MTLLGKKRTK TWHRGTLVAI KQVGNNLKYK
VRFENKGKSL LSGNHVAFEY HPTLERLFVG ARVVARYKDG NQVWLYAGVV AEMPNSKNRM
RFLIFFDDGY ASYVGLPELY PICRPLKKTW EDIEDASCRD FIEEYITSYP NRPMVLLKPG
QIIKTEWEGT WWKSRVEEVD GSLVKMLFLD DKRSEWIYRG STRLEPMFNL KMNTANSQEK
KMAGQQRQRP NMGALRTKGP VVQYTSDNSA AASTGGGAAT PGTPTRPVAP QPAGPPQPSR
TESPSFKSQM AKKSTGQLAL QPRQGMPSDL QPKPIINALQ TNTSRLFLLQ SGPVHTLTPI
TPAPQTVQTA ISTYTNERVP QEPSYQAPND RLFYLTHNCS PECLKRIRPT RPNLHRGRNP
LLTPLLYEFR RMTGRRRLNR KMSFHVIYKS PCGLSLRNMT EIQRYLFQTQ CDFIFLEMFC
LDPYVLVDRR FQPQRPFYFI RDITSGREDI PLSCVNEIDN TPPPSVAYSK ERIPEDGVYI
NTSADFLVGC DCTDGCRDKS KCSCHQLTLQ ATGCTPGGQI NPNAGYHYKR LDECLPTGIY
ECNKRCRCNM QMCTNRLVQH GLQVRLQLFK TQNKGWGIRC LDDIAKGSFV CIYAGKILTD
DFADKEGLEM GDEYFANLDH IESVENFKEG YESEAHCSDS EGSGVDMSRV KLPASSRHGK
SNKMEERNSS TTGKSQDDSS EESDDEKDDD SNEDDSDSSD DTFVKDTYYT TSSVWRSYTT
RRQAKGLKEE SQDSKDGMSV SAGEDRKPPH MPEETGKSKV ASWLTNQSST SANQSVKVEG
GIKTEKKDVM TLSDSDDVQT ISSGSDDNKE REKKTQAVVK RQVAVKSTRG IALKSHSMMV
KSGGGGAGGG GSGPSHGHGG GGGDNGPKNT RLFFDGEESC YIIDAKLEGN LGRYLNHSCS
PNLFVQNVFV DTHDLRFPWV AFFASKRIRA GTELTWDYNY EVGSVEGKEL LCCCGSTECR
GRLLQIIKTE WEGTWW
