ID SET1_SCHPO Reviewed; 920 AA.
AC Q9Y7R4;
DT 08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 27-MAR-2024, entry version 162.
DE RecName: Full=Histone-lysine N-methyltransferase, H3 lysine-4 specific;
DE EC=2.1.1.354 {ECO:0000269|PubMed:12589755};
DE AltName: Full=COMPASS component set1;
DE AltName: Full=Lysine N-methyltransferase 2;
DE AltName: Full=SET domain-containing protein 1;
DE AltName: Full=Set1 complex component set1;
DE Short=Set1C component set1;
DE AltName: Full=Spset1;
GN Name=set1 {ECO:0000312|EMBL:CAB41652.1}; Synonyms=kmt2;
GN ORFNames=SPCC306.04c;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1] {ECO:0000312|EMBL:CAB41652.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [2] {ECO:0000305}
RP FUNCTION.
RX PubMed=12193658; DOI=10.1073/pnas.182436399;
RA Noma K., Grewal S.I.S.;
RT "Histone H3 lysine 4 methylation is mediated by Set1 and promotes
RT maintenance of active chromatin states in fission yeast.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:16438-16445(2002).
RN [3] {ECO:0000305}
RP FUNCTION, AND IDENTIFICATION IN THE SET1 COMPLEX.
RX PubMed=12488447; DOI=10.1074/jbc.m209562200;
RA Roguev A., Schaft D., Shevchenko A., Aasland R., Shevchenko A.,
RA Stewart A.F.;
RT "High conservation of the Set1/Rad6 axis of histone 3 lysine 4 methylation
RT in budding and fission yeasts.";
RL J. Biol. Chem. 278:8487-8493(2003).
RN [4] {ECO:0000305}
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=12589755; DOI=10.1016/s0022-2836(03)00030-5;
RA Kanoh J., Francesconi S., Collura A., Schramke V., Ishikawa F.,
RA Baldacci G., Geli V.;
RT "The fission yeast spSet1p is a histone H3-K4 methyltransferase that
RT functions in telomere maintenance and DNA repair in an ATM kinase Rad3-
RT dependent pathway.";
RL J. Mol. Biol. 326:1081-1094(2003).
RN [5] {ECO:0000305}
RP IDENTIFICATION IN THE SET1 COMPLEX.
RX PubMed=14617822; DOI=10.1074/mcp.m300081-mcp200;
RA Roguev A., Shevchenko A., Schaft D., Thomas H., Stewart A.F.,
RA Shevchenko A.;
RT "A comparative analysis of an orthologous proteomic environment in the
RT yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe.";
RL Mol. Cell. Proteomics 3:125-132(2004).
CC -!- FUNCTION: Catalytic component of the COMPASS (Set1C) complex that
CC specifically mono-, di- and trimethylates histone H3 to form
CC H3K4me1/2/3 (PubMed:12589755, PubMed:12488447). Binds RNA which might
CC negatively affect its histone methyltransferase activity (By
CC similarity). COMPASS recognizes ubiquitinated H2B on one face of the
CC nucleosome which stimulates the methylation of H3 on the opposing face
CC (By similarity). Methylation promotes maintenance of active chromatin
CC states at euchromatic chromosomal domains and is present throughout the
CC cell cycle (PubMed:12193658). Plays a role in telomere maintenance and
CC DNA repair in an ATM kinase rad3-dependent pathway (PubMed:12589755).
CC Required for efficient telomeric and centromeric silencing
CC (PubMed:12589755). {ECO:0000250|UniProtKB:P38827,
CC ECO:0000269|PubMed:12193658, ECO:0000269|PubMed:12488447,
CC ECO:0000269|PubMed:12589755}.
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:12589755};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=N(6)-methyl-L-lysyl(4)-[histone H3] + S-adenosyl-L-methionine
CC = H(+) + N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:60268, Rhea:RHEA-COMP:15540, Rhea:RHEA-
CC COMP:15543, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:61929, ChEBI:CHEBI:61976;
CC Evidence={ECO:0000250|UniProtKB:P38827};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + S-adenosyl-L-
CC methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3]
CC + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60272, Rhea:RHEA-
CC COMP:15537, Rhea:RHEA-COMP:15540, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961,
CC ChEBI:CHEBI:61976; Evidence={ECO:0000250|UniProtKB:P38827};
CC -!- SUBUNIT: Component of the Set1C/COMPASS complex composed of ash2, sdc1,
CC set1, shg1, spp1, swd1, swd2 and swd3. {ECO:0000269|PubMed:12488447,
CC ECO:0000269|PubMed:14617822}.
CC -!- INTERACTION:
CC Q9Y7R4; Q9HDV4: lid2; NbExp=2; IntAct=EBI-2106005, EBI-2105919;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}. Chromosome {ECO:0000305}.
CC -!- DOMAIN: A construct containing set1 C-terminal fragment of 692-920 is
CC able to form H3K4me.
CC -!- DOMAIN: The RxxxRR motif forms an adapter helix that bridges the
CC nucleosome and ubiquitin. {ECO:0000250|UniProtKB:P38827}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CU329672; CAB41652.1; -; Genomic_DNA.
DR PIR; T41282; T41282.
DR RefSeq; NP_587812.1; NM_001022805.2.
DR AlphaFoldDB; Q9Y7R4; -.
DR SMR; Q9Y7R4; -.
DR BioGRID; 275345; 365.
DR ELM; Q9Y7R4; -.
DR IntAct; Q9Y7R4; 1.
DR STRING; 284812.Q9Y7R4; -.
DR iPTMnet; Q9Y7R4; -.
DR MaxQB; Q9Y7R4; -.
DR PaxDb; 4896-SPCC306-04c-1; -.
DR EnsemblFungi; SPCC306.04c.1; SPCC306.04c.1:pep; SPCC306.04c.
DR GeneID; 2538762; -.
DR KEGG; spo:SPCC306.04c; -.
DR PomBase; SPCC306.04c; set1.
DR VEuPathDB; FungiDB:SPCC306.04c; -.
DR eggNOG; KOG1080; Eukaryota.
DR HOGENOM; CLU_004391_1_0_1; -.
DR InParanoid; Q9Y7R4; -.
DR OMA; ERLPCLC; -.
DR PhylomeDB; Q9Y7R4; -.
DR Reactome; R-SPO-9772755; Formation of WDR5-containing histone-modifying complexes.
DR PRO; PR:Q9Y7R4; -.
DR Proteomes; UP000002485; Chromosome III.
DR GO; GO:0000785; C:chromatin; IC:PomBase.
DR GO; GO:0005737; C:cytoplasm; HDA:PomBase.
DR GO; GO:0048188; C:Set1C/COMPASS complex; IDA:PomBase.
DR GO; GO:0042800; F:histone H3K4 methyltransferase activity; IDA:PomBase.
DR GO; GO:0140999; F:histone H3K4 trimethyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0003723; F:RNA binding; ISM:PomBase.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0045815; P:transcription initiation-coupled chromatin remodeling; IC:PomBase.
DR CDD; cd00590; RRM_SF; 1.
DR CDD; cd12303; RRM_spSet1p_like; 1.
DR CDD; cd20072; SET_SET1; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR Gene3D; 2.170.270.10; SET domain; 1.
DR InterPro; IPR024657; COMPASS_Set1_N-SET.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR003616; Post-SET_dom.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR InterPro; IPR044570; Set1-like.
DR InterPro; IPR017111; Set1_fungi.
DR InterPro; IPR024636; SET_assoc.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR PANTHER; PTHR45814; HISTONE-LYSINE N-METHYLTRANSFERASE SETD1; 1.
DR PANTHER; PTHR45814:SF2; HISTONE-LYSINE N-METHYLTRANSFERASE SETD1; 1.
DR Pfam; PF11764; N-SET; 1.
DR Pfam; PF00076; RRM_1; 1.
DR Pfam; PF00856; SET; 1.
DR Pfam; PF11767; SET_assoc; 1.
DR PIRSF; PIRSF037104; Histone_H3-K4_mtfrase_Set1_fun; 1.
DR SMART; SM01291; N-SET; 1.
DR SMART; SM00508; PostSET; 1.
DR SMART; SM00360; RRM; 2.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF54928; RNA-binding domain, RBD; 2.
DR SUPFAM; SSF82199; SET domain; 1.
DR PROSITE; PS50868; POST_SET; 1.
DR PROSITE; PS50102; RRM; 1.
DR PROSITE; PS51572; SAM_MT43_1; 1.
DR PROSITE; PS50280; SET; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Chromosome; Methyltransferase; Nucleus;
KW Reference proteome; RNA-binding; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..920
FT /note="Histone-lysine N-methyltransferase, H3 lysine-4
FT specific"
FT /id="PRO_0000186085"
FT DOMAIN 94..179
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 781..898
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT DOMAIN 904..920
FT /note="Post-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT REGION 205..242
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 448..485
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 749..754
FT /note="RxxxRR motif"
FT /evidence="ECO:0000250|UniProtKB:P38827"
FT COMPBIAS 205..219
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 464..478
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 897
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
SQ SEQUENCE 920 AA; 105038 MW; C4AD7E6C3ECFF8BC CRC64;
MDFNTSTRSK SQPVQRNNYK VLYDPELGIK ENLGRKIIYR FNGVSKPPLV VRDPRLKNPI
YARGIPKSGR PFLKSLQTIN YDYNENSLGP EPPTQVFVSN ISPLVTSEQL RYHFKSFGEV
FDLDLKLNPY TGTSLGLCCI SFDKRSSISV AAHSAKIAVQ QANGLRFSGK PLSVVLDRDG
SLCEEAFKKA LNAVEKQFQE ETLQKQRFER EDESSRQKLS AAMNEDIPPW RQPSKNSQTL
SNGDLQHSKV QNVDQKSGFL TSSETDVPKN INDYIYLLID DRFVPPDRVY YTDIKHHFRK
FLYEKIYMNK DGFYITFNNY REASNCYRAL DRTYVQNCRI KLKFHDIPSR TKEDGKKSAV
RRVVLPPEEA YAEATSVVLR DLEAALLRDV KSKIIGPAIF KYLHSMPKPS VKEELQENLL
VSSTSVPDVP LKIESTVGKL PSLPKFKKRV DSSKMNLSAG SKTKSKLQRR RRRRHEARPL
HYQLNQMYNS SASEAESDQE LLLSSGDERV ERGKIGSIKS VKSDEATPVF SDTSDENDKF
HRFRTKSKIS KKKYEKMEVD YTSSSETESD ASILSPSAAI PKSGSAIKDE LISPKKEIDE
VLALAPKWRI NEFDETGSVY YGALPYNYPE DDVLLDLDGL QYLVKNDEDY SYLQEALKDE
PLMDINDPNF WAYERKSCKF KNGDVKYGDT AILPEPKGYF RSNTSGSAKS EGYYIIPTTE
KSLYLPLRNR STIDTISHST SRITSRMNRV NNRRLAAGVE KSQLPAEADL LRFNALKARK
KQLHFGPSRI HTLGLFAMEN IDKNDMVIEY IGEIIRQRVA DNREKNYVRE GIGDSYLFRI
DEDVIVDATK KGNIARFINH SCAPNCIARI IRVEGKRKIV IYADRDIMHG EELTYDYKFP
EEADKIPCLC GAPTCRGYLN
//
