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Histone-lysine N-methyltransferase met-2 (EC 2.1.1.43)

 MET2_CAEEL              Reviewed;        1304 AA.
P34544; Q8WTP5;
01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
14-MAY-2014, sequence version 5.
22-NOV-2017, entry version 133.
RecName: Full=Histone-lysine N-methyltransferase met-2;
EC=2.1.1.43;
Name=met-2; ORFNames=R05D3.11;
Caenorhabditis elegans.
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
NCBI_TaxID=6239;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Bristol N2;
PubMed=7906398; DOI=10.1038/368032a0;
Wilson R., Ainscough R., Anderson K., Baynes C., Berks M.,
Bonfield J., Burton J., Connell M., Copsey T., Cooper J., Coulson A.,
Craxton M., Dear S., Du Z., Durbin R., Favello A., Fraser A.,
Fulton L., Gardner A., Green P., Hawkins T., Hillier L., Jier M.,
Johnston L., Jones M., Kershaw J., Kirsten J., Laisster N.,
Latreille P., Lightning J., Lloyd C., Mortimore B., O'Callaghan M.,
Parsons J., Percy C., Rifken L., Roopra A., Saunders D., Shownkeen R.,
Sims M., Smaldon N., Smith A., Smith M., Sonnhammer E., Staden R.,
Sulston J., Thierry-Mieg J., Thomas K., Vaudin M., Vaughan K.,
Waterston R., Watson A., Weinstock L., Wilkinson-Sproat J.,
Wohldman P.;
"2.2 Mb of contiguous nucleotide sequence from chromosome III of C.
elegans.";
Nature 368:32-38(1994).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Bristol N2;
PubMed=9851916; DOI=10.1126/science.282.5396.2012;
The C. elegans sequencing consortium;
"Genome sequence of the nematode C. elegans: a platform for
investigating biology.";
Science 282:2012-2018(1998).
[3]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=15990876; DOI=10.1038/sj.emboj.7600726;
Poulin G., Dong Y., Fraser A.G., Hopper N.A., Ahringer J.;
"Chromatin regulation and sumoylation in the inhibition of Ras-induced
vulval development in Caenorhabditis elegans.";
EMBO J. 24:2613-2623(2005).
[4]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=17634190; DOI=10.1242/dev.009373;
Andersen E.C., Horvitz H.R.;
"Two C. elegans histone methyltransferases repress lin-3 EGF
transcription to inhibit vulval development.";
Development 134:2991-2999(2007).
[5]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=20107519; DOI=10.1371/journal.pgen.1000830;
Bessler J.B., Andersen E.C., Villeneuve A.M.;
"Differential localization and independent acquisition of the H3K9me2
and H3K9me3 chromatin modifications in the Caenorhabditis elegans
adult germ line.";
PLoS Genet. 6:E1000830-E1000830(2010).
[6]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=21437264; DOI=10.1371/journal.pgen.1002017;
Koester-Eiserfunke N., Fischle W.;
"H3K9me2/3 binding of the MBT domain protein LIN-61 is essential for
Caenorhabditis elegans vulva development.";
PLoS Genet. 7:E1002017-E1002017(2011).
[7]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=21909284; DOI=10.1371/journal.pgen.1002267;
Checchi P.M., Engebrecht J.;
"Caenorhabditis elegans histone methyltransferase MET-2 shields the
male X chromosome from checkpoint machinery and mediates meiotic sex
chromosome inactivation.";
PLoS Genet. 7:E1002267-E1002267(2011).
[8]
FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
PubMed=22939621; DOI=10.1016/j.cell.2012.06.051;
Towbin B.D., Gonzalez-Aguilera C., Sack R., Gaidatzis D., Kalck V.,
Meister P., Askjaer P., Gasser S.M.;
"Step-wise methylation of histone H3K9 positions heterochromatin at
the nuclear periphery.";
Cell 150:934-947(2012).
[9]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=24685137; DOI=10.1016/j.celrep.2014.02.044;
Greer E.L., Beese-Sims S.E., Brookes E., Spadafora R., Zhu Y.,
Rothbart S.B., Aristizabal-Corrales D., Chen S., Badeaux A.I., Jin Q.,
Wang W., Strahl B.D., Colaiacovo M.P., Shi Y.;
"A histone methylation network regulates transgenerational epigenetic
memory in C. elegans.";
Cell Rep. 7:113-126(2014).
[10]
FUNCTION.
PubMed=26365259; DOI=10.1016/j.cub.2015.07.051;
Mao H., Zhu C., Zong D., Weng C., Yang X., Huang H., Liu D., Feng X.,
Guang S.;
"The Nrde pathway mediates small-RNA-directed histone H3 lysine 27
trimethylation in Caenorhabditis elegans.";
Curr. Biol. 25:2398-2403(2015).
[11]
FUNCTION.
PubMed=27668659; DOI=10.1038/ng.3672;
Zeller P., Padeken J., van Schendel R., Kalck V., Tijsterman M.,
Gasser S.M.;
"Histone H3K9 methylation is dispensable for Caenorhabditis elegans
development but suppresses RNA:DNA hybrid-associated repeat
instability.";
Nat. Genet. 48:1385-1395(2016).
-!- FUNCTION: Histone methyltransferase which is required for the
mono- and dimethylation of 'Lys-9' of histone H3 (PubMed:20107519,
PubMed:22939621). This increases the efficiency of set-25-mediated
trimethylation of histone H3 'Lys-9' (PubMed:22939621). Involved
in the transcriptional repression of lin-3 which is required for
the negative regulation of vulval cell fate specification during
postembryonic development (PubMed:17634190). Has a role in
blocking checkpoint signaling and mediating the transcriptional
silencing of meiotic sex chromosome inactivation; a mechanism
which enables checkpoint proteins to distinguish between the
partnerless male X chromosome and asynapsed chromosomes thereby
shielding the lone X from inappropriate activation of an apoptotic
program (PubMed:21909284). Operates redundantly with set-25 to
position chromatin at the nuclear periphery (PubMed:22939621).
Required for small-RNA-induced H3K9 methylation (PubMed:26365259).
Together with set-25, protects and stabilizes repeat-rich genomic
regions by suppressing transcription-induced replication stress
through methylation of H3K9 (PubMed:27668659). Together with spr-
5, required for transgenerational fertility (PubMed:24685137).
{ECO:0000269|PubMed:15990876, ECO:0000269|PubMed:17634190,
ECO:0000269|PubMed:20107519, ECO:0000269|PubMed:21437264,
ECO:0000269|PubMed:21909284, ECO:0000269|PubMed:22939621,
ECO:0000269|PubMed:24685137, ECO:0000269|PubMed:26365259,
ECO:0000269|PubMed:27668659}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] =
S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22939621}.
Chromosome {ECO:0000305|PubMed:22939621}. Cytoplasm
{ECO:0000269|PubMed:22939621}.
-!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that
are arranged in a triangular cluster; some of these Cys residues
contribute to the binding of two zinc ions within the cluster.
{ECO:0000250}.
-!- DISRUPTION PHENOTYPE: Induced vulval precursor cells in the
absence of lin-15A (PubMed:15990876). Multi-vulval phenotype is
apparent when grown at 24.5 degrees Celsius in the absence of lin-
61 and when grown at 20 degrees Celsius in the absence of hpl-2 or
met-1 (PubMed:17634190, PubMed:21437264). Reduced lamin
interaction of chromosome arms in the absence of set-25
(PubMed:22939621). Increased apoptosis and increased occurrence of
the recombination checkpoint XO germ lines (PubMed:21909284). High
incidence of endomitotic oocytes (PubMed:20107519). In spr-5 null
mutants, accelerates the progressive sterility over generations,
which is seen in spr-5 mutants with complete sterility achieved by
generation 2 (PubMed:24685137). {ECO:0000269|PubMed:15990876,
ECO:0000269|PubMed:17634190, ECO:0000269|PubMed:20107519,
ECO:0000269|PubMed:21437264, ECO:0000269|PubMed:21909284,
ECO:0000269|PubMed:22939621, ECO:0000269|PubMed:24685137}.
-!- SIMILARITY: Belongs to the class V-like SAM-binding
methyltransferase superfamily. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; FO081667; CCD73198.2; -; Genomic_DNA.
RefSeq; NP_498848.4; NM_066447.5.
SMR; P34544; -.
STRING; 6239.R05D3.11; -.
EPD; P34544; -.
PaxDb; P34544; -.
PeptideAtlas; P34544; -.
PRIDE; P34544; -.
EnsemblMetazoa; R05D3.11; R05D3.11; WBGene00019883.
GeneID; 176183; -.
KEGG; cel:CELE_R05D3.11; -.
UCSC; R05D3.11; c. elegans.
CTD; 176183; -.
WormBase; R05D3.11; CE47959; WBGene00019883; met-2.
eggNOG; KOG1141; Eukaryota.
eggNOG; COG2940; LUCA.
GeneTree; ENSGT00780000121845; -.
HOGENOM; HOG000021401; -.
InParanoid; P34544; -.
OMA; RVVQNNI; -.
OrthoDB; EOG091G014F; -.
PRO; PR:P34544; -.
Proteomes; UP000001940; Chromosome III.
Bgee; WBGene00019883; -.
GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
GO; GO:0005737; C:cytoplasm; IDA:WormBase.
GO; GO:0005634; C:nucleus; IC:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IC:UniProtKB.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0010452; P:histone H3-K36 methylation; IMP:WormBase.
GO; GO:0051567; P:histone H3-K9 methylation; IMP:WormBase.
GO; GO:0051321; P:meiotic cell cycle; IEA:UniProtKB-KW.
GO; GO:0010629; P:negative regulation of gene expression; IMP:UniProtKB.
GO; GO:0045835; P:negative regulation of meiotic nuclear division; IMP:UniProtKB.
GO; GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IGI:WormBase.
GO; GO:0040027; P:negative regulation of vulval development; IGI:WormBase.
GO; GO:0040029; P:regulation of gene expression, epigenetic; IMP:WormBase.
GO; GO:0007548; P:sex differentiation; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0072325; P:vulval cell fate commitment; IMP:UniProtKB.
InterPro; IPR016177; DNA-bd_dom_sf.
InterPro; IPR001739; Methyl_CpG_DNA-bd.
InterPro; IPR003616; Post-SET_dom.
InterPro; IPR007728; Pre-SET_dom.
InterPro; IPR001214; SET_dom.
Pfam; PF01429; MBD; 1.
Pfam; PF05033; Pre-SET; 1.
Pfam; PF00856; SET; 1.
SMART; SM00391; MBD; 1.
SMART; SM00508; PostSET; 1.
SMART; SM00468; PreSET; 1.
SMART; SM00317; SET; 1.
SUPFAM; SSF54171; SSF54171; 1.
PROSITE; PS50982; MBD; 1.
PROSITE; PS50868; POST_SET; 1.
PROSITE; PS50867; PRE_SET; 1.
PROSITE; PS50280; SET; 1.
3: Inferred from homology;
Chromosome; Coiled coil; Complete proteome; Cytoplasm;
Differentiation; Meiosis; Metal-binding; Methyltransferase; Nucleus;
Reference proteome; Repeat; S-adenosyl-L-methionine;
Sexual differentiation; Transcription; Transcription regulation;
Transferase; Zinc.
CHAIN 1 1304 Histone-lysine N-methyltransferase met-2.
/FTId=PRO_0000186066.
DOMAIN 834 909 MBD. {ECO:0000255|PROSITE-
ProRule:PRU00338}.
DOMAIN 971 1049 Pre-SET. {ECO:0000255|PROSITE-
ProRule:PRU00157}.
DOMAIN 1052 1277 SET. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
DOMAIN 1286 1302 Post-SET. {ECO:0000255|PROSITE-
ProRule:PRU00155}.
REGION 1062 1064 S-adenosyl-L-methionine binding.
{ECO:0000250}.
REGION 1234 1235 S-adenosyl-L-methionine binding.
{ECO:0000250}.
COILED 97 129 {ECO:0000255}.
METAL 973 973 Zinc 1. {ECO:0000250}.
METAL 973 973 Zinc 2. {ECO:0000250}.
METAL 975 975 Zinc 1. {ECO:0000250}.
METAL 979 979 Zinc 1. {ECO:0000250}.
METAL 979 979 Zinc 3. {ECO:0000250}.
METAL 985 985 Zinc 1. {ECO:0000250}.
METAL 987 987 Zinc 2. {ECO:0000250}.
METAL 1030 1030 Zinc 2. {ECO:0000250}.
METAL 1030 1030 Zinc 3. {ECO:0000250}.
METAL 1034 1034 Zinc 2. {ECO:0000250}.
METAL 1036 1036 Zinc 3. {ECO:0000250}.
METAL 1041 1041 Zinc 3. {ECO:0000250}.
METAL 1237 1237 Zinc 4. {ECO:0000250}.
METAL 1290 1290 Zinc 4. {ECO:0000250}.
METAL 1292 1292 Zinc 4. {ECO:0000250}.
METAL 1297 1297 Zinc 4. {ECO:0000250}.
BINDING 1098 1098 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
BINDING 1100 1100 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
BINDING 1231 1231 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
SEQUENCE 1304 AA; 148155 MW; E7D229260AF88A20 CRC64;
MDQQEPSNNV DTSSILSDDG METQEQSSFV TATIDLTVDD YDETEIQEIL DNGKAEEGTD
EDSDLVEGIL NANSDVQALL DAPSEQVAQA LNSFFGNESE QEAVAAQRRV DAEKTAKDEA
ELKQQEEAED LIIEDSIVKT DEEKQAVRRL KINEFLSWFT RLLPEQFKNF EFTNPNYLTE
SISDSPVVNV DKCKEIVKSF KESESLEGLS QKYELIDEDV LVAAICIGVL DTNNEEDVDF
NVLCDDRIDD WSIEKCVTFL DYPNTGLNSK NGPLRFMQFT VTSPASAILM LTLIRLREEG
HPCRLDFDSN PTDDLLLNFD QVEFSNNIID TAVKYWDDQK ENGAQDKIGR ELNDFFHEIE
STSAEFKQHF ENAVGSRNEI IQLVNEKIPD FDGTEAAVNE SFTSDQRTEI INSRAIMETL
KAEMKLAIAE AQKVYDTKTD FEKFFVLTVG DFCLARANPS DDAELTYAIV QDRVDAMTYK
VKFIDTSQIR ECNIRDLAMT TQGMYDPSLN TFGDVGLRVA CRQVISSSQF GKKTIWLTGT
AAGRRRAHRS DFLIFFDNGT DAYVSAPTMP GEPGYEVASE KKSVFSLKEM IAKMNAAQIA
IMVGQPVGKE GNLDYFLTFH WIRQSHRSAY IRDFMKEFPE WPLLKMPVGM RICLYNSLVD
RRKKMVTVIG TDRAFAIVRH EAPNPLAPGN RCTDFPCNDR NHQHIDEKIY RGSHRLEGAA
HKKHMISTNN NLSQRRKDQL QSQFEPTDMI RSMPERNHQQ VVKKKTTGTN QNVASTNDAK
SKREIEIRKK NQFLFNKIIV PIPVLTPLEN LKAHAQCGPD CLQKMDADPY EARFHRNSPI
HTPLLCGWRR IMYTMSTGKK RGAVKKNIIY FSPCGAALHQ ISDVSEYIHV TRSLLTIDCF
SFDARIDTAT YITVDDKYLK VADFSLGTEG IPIPLVNSVD NDEPPSLEYS KRRFQYNDQV
DISSVSRDFC SGCSCDGDCS DASKCECQQL SIEAMKRLPH NLQFDGHDEL VPHYQNRLLS
SKVISGLYEC NDQCSCHRKS CYNRVVQNNI KYPMHIFKTA QSGWGVRALT DIPQSTFICT
YVGAILTDDL ADELRNADQY FADLDLKDTV ELEKGREDHE TDFGYGGDES DYDDEEGSDG
DSGDDVMNKM VKRQDSSESG EETKRLTRQK RKQSKKSGKG GSVEKDDTTP RDSMEKDNIE
SKDEPVFNWD KYFEPFPLYV IDAKQRGNLG RFLNHSCDPN VHVQHVMYDT HDLRLPWVAF
FTRKYVKAGD ELTWDYQYTQ DQTATTQLTC HCGAENCTGR LLKS


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