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Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 (EC 2.1.1.43) (Histone H3-K9 methyltransferase 4) (H3-K9-HMTase 4) (Protein KRYPTONITE) (Protein SET DOMAIN GROUP 33) (Suppressor of variegation 3-9 homolog protein 4) (Su(var)3-9 homolog protein 4)

 SUVH4_ARATH             Reviewed;         624 AA.
Q8GZB6; Q9C5P3; Q9FFX9;
09-MAY-2003, integrated into UniProtKB/Swiss-Prot.
09-MAY-2003, sequence version 2.
22-NOV-2017, entry version 127.
RecName: Full=Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4;
EC=2.1.1.43;
AltName: Full=Histone H3-K9 methyltransferase 4;
Short=H3-K9-HMTase 4;
AltName: Full=Protein KRYPTONITE;
AltName: Full=Protein SET DOMAIN GROUP 33;
AltName: Full=Suppressor of variegation 3-9 homolog protein 4;
Short=Su(var)3-9 homolog protein 4;
Name=SUVH4; Synonyms=KYP, SDG33, SET33; OrderedLocusNames=At5g13960;
ORFNames=MAC12.7;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA], NOMENCLATURE, AND TISSUE SPECIFICITY.
PubMed=11691919; DOI=10.1093/nar/29.21.4319;
Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K.,
Assalkhou R., Schulz I., Reuter G., Aalen R.B.;
"The Arabidopsis thaliana genome contains at least 29 active genes
encoding SET domain proteins that can be assigned to four
evolutionarily conserved classes.";
Nucleic Acids Res. 29:4319-4333(2001).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=cv. Wassilewskija;
PubMed=12486005; DOI=10.1093/emboj/cdf687;
Malagnac F., Bartee L., Bender J.;
"An Arabidopsis SET domain protein required for maintenance but not
establishment of DNA methylation.";
EMBO J. 21:6842-6852(2002).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=9330910; DOI=10.1093/dnares/4.3.215;
Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
Miyajima N., Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
features of the 1.6 Mb regions covered by twenty physically assigned
P1 clones.";
DNA Res. 4:215-230(1997).
[4]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[6]
FUNCTION, AND MUTANTS KYP-1; KYP-2 AND KYP-3.
PubMed=11898023; DOI=10.1038/nature731;
Jackson J.P., Lindroth A.M., Cao X., Jacobsen S.E.;
"Control of CpNpG DNA methylation by the KRYPTONITE histone H3
methyltransferase.";
Nature 416:556-560(2002).
[7]
EPIGENETIC METHYLATION.
PubMed=12194816; DOI=10.1016/S0960-9822(02)00976-4;
Johnson L.M., Cao X., Jacobsen S.E.;
"Interplay between two epigenetic marks: DNA methylation and histone
H3 lysine 9 methylation.";
Curr. Biol. 12:1360-1367(2002).
[8]
FUNCTION.
PubMed=15457214; DOI=10.1038/sj.emboj.7600430;
Lindroth A.M., Shultis D., Jasencakova Z., Fuchs J., Johnson L.,
Schubert D., Patnaik D., Pradhan S., Goodrich J., Schubert I.,
Jenuwein T., Khorasanizadeh S., Jacobsen S.E.;
"Dual histone H3 methylation marks at lysines 9 and 27 required for
interaction with CHROMOMETHYLASE3.";
EMBO J. 23:4286-4296(2004).
[9]
FUNCTION.
PubMed=15598823; DOI=10.1093/nar/gkh992;
Johnson L., Mollah S., Garcia B.A., Muratore T.L., Shabanowitz J.,
Hunt D.F., Jacobsen S.E.;
"Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct
combinations of post-translational modifications.";
Nucleic Acids Res. 32:6511-6518(2004).
[10]
FUNCTION.
PubMed=16277745; DOI=10.1186/gb-2005-6-11-r90;
Tran R.K., Zilberman D., de Bustos C., Ditt R.F., Henikoff J.G.,
Lindroth A.M., Delrow J., Boyle T., Kwong S., Bryson T.D.,
Jacobsen S.E., Henikoff S.;
"Chromatin and siRNA pathways cooperate to maintain DNA methylation of
small transposable elements in Arabidopsis.";
Genome Biol. 6:R90.1-R90.11(2005).
[11]
FUNCTION.
PubMed=16287862; DOI=10.1128/MCB.25.23.10507-10515.2005;
Ebbs M.L., Bartee L., Bender J.;
"H3 lysine 9 methylation is maintained on a transcribed inverted
repeat by combined action of SUVH6 and SUVH4 methyltransferases.";
Mol. Cell. Biol. 25:10507-10515(2005).
[12]
GENE FAMILY.
PubMed=16384625; DOI=10.1016/j.jplph.2005.10.015;
Fischer A., Hofmann I., Naumann K., Reuter G.;
"Heterochromatin proteins and the control of heterochromatic gene
silencing in Arabidopsis.";
J. Plant Physiol. 163:358-368(2006).
-!- FUNCTION: Histone methyltransferase. Methylates 'Lys-9' of histone
H3. H3 'Lys-9' methylation represents a specific tag for
epigenetic transcriptional repression. The silencing mechanism via
DNA CpNpG methylation requires the targeting of chromomethylase
CMT3 to methylated histones, probably through an interaction with
an HP1-like adapter. By its function, KYP is directly required for
the maintenance of the DNA CpNpG and asymmetric methylation.
Involved in the silencing of transposable elements.
{ECO:0000269|PubMed:11898023, ECO:0000269|PubMed:15457214,
ECO:0000269|PubMed:15598823, ECO:0000269|PubMed:16277745,
ECO:0000269|PubMed:16287862}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] =
S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
{ECO:0000255|PROSITE-ProRule:PRU00908}.
-!- SUBUNIT: Interacts with H3 histone.
-!- INTERACTION:
P03562:AL2 (xeno); NbExp=4; IntAct=EBI-16175525, EBI-16175508;
Q96703:AL2 (xeno); NbExp=2; IntAct=EBI-16175525, EBI-16175606;
-!- SUBCELLULAR LOCATION: Nucleus. Chromosome. Chromosome, centromere.
Note=Associates with centromeric constitutive heterochromatin and
at a lower level with regions of euchromatin.
-!- TISSUE SPECIFICITY: Expressed in leaves stems and flowers.
{ECO:0000269|PubMed:11691919}.
-!- DOMAIN: Although the SET domain contains the active site of
enzymatic activity, both pre-SET and post-SET domains are required
for methyltransferase activity.
-!- 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}.
-!- MISCELLANEOUS: Mutations in the KYP/SUVH4 gene decrease the level
of histone H3-K9 dimethylated, trimethylated or dimethylated in
association with H3-K14Ac by factors of 4,3 and 3, respectively.
The level of monomethylated H3-K9 is unchanged. Such mutations
lead to a drastic decrease of cytosine methylation at CpNpG sites,
causing the reactivation of endogenous retrotransposons. The
KRYPTONYTE methyltransferase name was given according to its
involvement in SUPERMAN gene silencing.
-!- SIMILARITY: Belongs to the class V-like SAM-binding
methyltransferase superfamily. Histone-lysine methyltransferase
family. Suvar3-9 subfamily. {ECO:0000255|PROSITE-
ProRule:PRU00908}.
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EMBL; AF344447; AAK28969.1; -; mRNA.
EMBL; AF538715; AAO17392.1; -; Genomic_DNA.
EMBL; AB005230; BAB11124.1; -; Genomic_DNA.
EMBL; CP002688; AED91966.1; -; Genomic_DNA.
EMBL; BT002313; AAN86146.1; -; mRNA.
RefSeq; NP_196900.1; NM_121399.3.
UniGene; At.8330; -.
PDB; 4QEN; X-ray; 2.00 A; A=93-624.
PDB; 4QEO; X-ray; 2.00 A; A=93-624.
PDB; 4QEP; X-ray; 3.10 A; A=93-624.
PDBsum; 4QEN; -.
PDBsum; 4QEO; -.
PDBsum; 4QEP; -.
ProteinModelPortal; Q8GZB6; -.
SMR; Q8GZB6; -.
BioGrid; 16522; 1.
DIP; DIP-62058N; -.
IntAct; Q8GZB6; 3.
STRING; 3702.AT5G13960.1; -.
iPTMnet; Q8GZB6; -.
PaxDb; Q8GZB6; -.
EnsemblPlants; AT5G13960.1; AT5G13960.1; AT5G13960.
GeneID; 831244; -.
Gramene; AT5G13960.1; AT5G13960.1; AT5G13960.
KEGG; ath:AT5G13960; -.
Araport; AT5G13960; -.
TAIR; locus:2159133; AT5G13960.
eggNOG; KOG1082; Eukaryota.
eggNOG; COG2940; LUCA.
eggNOG; COG3440; LUCA.
HOGENOM; HOG000238382; -.
InParanoid; Q8GZB6; -.
KO; K11420; -.
OMA; GMKYQGK; -.
OrthoDB; EOG09360A66; -.
PhylomeDB; Q8GZB6; -.
BioCyc; ARA:AT5G13960-MONOMER; -.
Reactome; R-ATH-3214841; PKMTs methylate histone lysines.
PRO; PR:Q8GZB6; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q8GZB6; baseline and differential.
Genevisible; Q8GZB6; AT.
GO; GO:0000775; C:chromosome, centromeric region; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0010385; F:double-stranded methylated DNA binding; IDA:TAIR.
GO; GO:0046974; F:histone methyltransferase activity (H3-K9 specific); IDA:TAIR.
GO; GO:0008327; F:methyl-CpG binding; IDA:TAIR.
GO; GO:0010428; F:methyl-CpNpG binding; IDA:TAIR.
GO; GO:0010429; F:methyl-CpNpN binding; IDA:TAIR.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0051567; P:histone H3-K9 methylation; IMP:TAIR.
GO; GO:0016571; P:histone methylation; IDA:TAIR.
GO; GO:0010216; P:maintenance of DNA methylation; IDA:TAIR.
GO; GO:0018022; P:peptidyl-lysine methylation; IDA:TAIR.
Gene3D; 2.30.280.10; -; 1.
InterPro; IPR025794; Hist-Lys_N-MeTrfase_plant.
InterPro; IPR003616; Post-SET_dom.
InterPro; IPR007728; Pre-SET_dom.
InterPro; IPR015947; PUA-like_sf.
InterPro; IPR001214; SET_dom.
InterPro; IPR036987; SRA-YDG_sf.
InterPro; IPR003105; SRA_YDG.
Pfam; PF05033; Pre-SET; 1.
Pfam; PF02182; SAD_SRA; 1.
Pfam; PF00856; SET; 1.
SMART; SM00468; PreSET; 1.
SMART; SM00317; SET; 1.
SMART; SM00466; SRA; 1.
SUPFAM; SSF88697; SSF88697; 1.
PROSITE; PS50868; POST_SET; 1.
PROSITE; PS50867; PRE_SET; 1.
PROSITE; PS51575; SAM_MT43_SUVAR39_2; 1.
PROSITE; PS50280; SET; 1.
PROSITE; PS51015; YDG; 1.
1: Evidence at protein level;
3D-structure; Centromere; Chromatin regulator; Chromosome;
Complete proteome; Metal-binding; Methyltransferase; Nucleus;
Reference proteome; S-adenosyl-L-methionine; Transferase; Zinc.
CHAIN 1 624 Histone-lysine N-methyltransferase, H3
lysine-9 specific SUVH4.
/FTId=PRO_0000186075.
DOMAIN 149 302 YDG. {ECO:0000255|PROSITE-
ProRule:PRU00358}.
DOMAIN 381 443 Pre-SET. {ECO:0000255|PROSITE-
ProRule:PRU00157}.
DOMAIN 446 594 SET. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
DOMAIN 608 624 Post-SET. {ECO:0000255|PROSITE-
ProRule:PRU00155}.
REGION 456 458 S-adenosyl-L-methionine binding.
{ECO:0000250}.
REGION 551 552 S-adenosyl-L-methionine binding.
{ECO:0000250}.
METAL 383 383 Zinc 1. {ECO:0000250}.
METAL 383 383 Zinc 2. {ECO:0000250}.
METAL 385 385 Zinc 1. {ECO:0000250}.
METAL 389 389 Zinc 1. {ECO:0000250}.
METAL 389 389 Zinc 3. {ECO:0000250}.
METAL 395 395 Zinc 1. {ECO:0000250}.
METAL 397 397 Zinc 2. {ECO:0000250}.
METAL 425 425 Zinc 2. {ECO:0000250}.
METAL 425 425 Zinc 3. {ECO:0000250}.
METAL 429 429 Zinc 2. {ECO:0000250}.
METAL 431 431 Zinc 3. {ECO:0000250}.
METAL 435 435 Zinc 3. {ECO:0000250}.
METAL 554 554 Zinc 4. {ECO:0000250}.
METAL 612 612 Zinc 4. {ECO:0000250}.
METAL 614 614 Zinc 4. {ECO:0000250}.
METAL 619 619 Zinc 4. {ECO:0000250}.
BINDING 493 493 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
BINDING 548 548 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
CONFLICT 189 189 E -> D (in Ref. 2; AAO17392).
{ECO:0000305}.
CONFLICT 548 548 R -> T (in Ref. 1; AAK28969).
{ECO:0000305}.
CONFLICT 576 576 V -> A (in Ref. 1; AAK28969).
{ECO:0000305}.
HELIX 101 121 {ECO:0000244|PDB:4QEO}.
HELIX 127 137 {ECO:0000244|PDB:4QEO}.
STRAND 159 162 {ECO:0000244|PDB:4QEO}.
HELIX 163 168 {ECO:0000244|PDB:4QEO}.
STRAND 170 172 {ECO:0000244|PDB:4QEN}.
STRAND 178 182 {ECO:0000244|PDB:4QEO}.
HELIX 184 186 {ECO:0000244|PDB:4QEO}.
TURN 187 192 {ECO:0000244|PDB:4QEO}.
STRAND 197 203 {ECO:0000244|PDB:4QEO}.
STRAND 211 213 {ECO:0000244|PDB:4QEO}.
STRAND 216 220 {ECO:0000244|PDB:4QEO}.
STRAND 222 225 {ECO:0000244|PDB:4QEO}.
STRAND 227 230 {ECO:0000244|PDB:4QEN}.
STRAND 239 241 {ECO:0000244|PDB:4QEP}.
HELIX 242 252 {ECO:0000244|PDB:4QEO}.
STRAND 256 263 {ECO:0000244|PDB:4QEO}.
STRAND 271 288 {ECO:0000244|PDB:4QEO}.
STRAND 292 302 {ECO:0000244|PDB:4QEO}.
STRAND 304 306 {ECO:0000244|PDB:4QEO}.
STRAND 331 334 {ECO:0000244|PDB:4QEO}.
STRAND 336 339 {ECO:0000244|PDB:4QEN}.
STRAND 341 343 {ECO:0000244|PDB:4QEO}.
TURN 358 361 {ECO:0000244|PDB:4QEO}.
STRAND 386 388 {ECO:0000244|PDB:4QEO}.
TURN 392 394 {ECO:0000244|PDB:4QEO}.
HELIX 396 400 {ECO:0000244|PDB:4QEO}.
STRAND 406 410 {ECO:0000244|PDB:4QEO}.
STRAND 420 423 {ECO:0000244|PDB:4QEP}.
HELIX 436 441 {ECO:0000244|PDB:4QEO}.
STRAND 448 452 {ECO:0000244|PDB:4QEO}.
STRAND 454 456 {ECO:0000244|PDB:4QEO}.
STRAND 458 464 {ECO:0000244|PDB:4QEO}.
STRAND 471 474 {ECO:0000244|PDB:4QEO}.
STRAND 477 481 {ECO:0000244|PDB:4QEO}.
HELIX 482 484 {ECO:0000244|PDB:4QEO}.
STRAND 494 496 {ECO:0000244|PDB:4QEO}.
STRAND 536 539 {ECO:0000244|PDB:4QEO}.
STRAND 541 544 {ECO:0000244|PDB:4QEO}.
HELIX 546 549 {ECO:0000244|PDB:4QEO}.
STRAND 557 567 {ECO:0000244|PDB:4QEO}.
HELIX 570 572 {ECO:0000244|PDB:4QEO}.
STRAND 574 581 {ECO:0000244|PDB:4QEO}.
STRAND 603 605 {ECO:0000244|PDB:4QEO}.
SEQUENCE 624 AA; 70056 MW; 67B5CF6606F16B07 CRC64;
MAGKRKRANA PDQTERRSSV RVQKVRQKAL DEKARLVQER VKLLSDRKSE ICVDDTELHE
KEEENVDGSP KRRSPPKLTA MQKGKQKLSV SLNGKDVNLE PHLKVTKCLR LFNKQYLLCV
QAKLSRPDLK GVTEMIKAKA ILYPRKIIGD LPGIDVGHRF FSRAEMCAVG FHNHWLNGID
YMSMEYEKEY SNYKLPLAVS IVMSGQYEDD LDNADTVTYT GQGGHNLTGN KRQIKDQLLE
RGNLALKHCC EYNVPVRVTR GHNCKSSYTK RVYTYDGLYK VEKFWAQKGV SGFTVYKYRL
KRLEGQPELT TDQVNFVAGR IPTSTSEIEG LVCEDISGGL EFKGIPATNR VDDSPVSPTS
GFTYIKSLII EPNVIIPKSS TGCNCRGSCT DSKKCACAKL NGGNFPYVDL NDGRLIESRD
VVFECGPHCG CGPKCVNRTS QKRLRFNLEV FRSAKKGWAV RSWEYIPAGS PVCEYIGVVR
RTADVDTISD NEYIFEIDCQ QTMQGLGGRQ RRLRDVAVPM NNGVSQSSED ENAPEFCIDA
GSTGNFARFI NHSCEPNLFV QCVLSSHQDI RLARVVLFAA DNISPMQELT YDYGYALDSV
HGPDGKVKQL ACYCGALNCR KRLY


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EIAAB12655 BAT8,C6orf30,EHMT2,Euchromatic histone-lysine N-methyltransferase 2,G9A,H3-K9-HMTase 3,Histone H3-K9 methyltransferase 3,Histone-lysine N-methyltransferase EHMT2,HLA-B-associated transcript 8,Homo sap
EIAAB27930 Androgen receptor coactivator 267 kDa protein,Androgen receptor-associated protein of 267 kDa,ARA267,H3-K36-HMTase,H4-K20-HMTase,Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 speci
EIAAB37976 H3-K4-HMTase SETD7,Histone H3-K4 methyltransferase SETD7,Histone-lysine N-methyltransferase SETD7,Kiaa1717,Mouse,Mus musculus,SET domain-containing protein 7,Set7,SET7_9,Set9,Setd7
EIAAB24943 Histone-lysine N-methyltransferase MLL4,Mll2,Mouse,Mus musculus,Myeloid_lymphoid or mixed-lineage leukemia protein 4 homolog,Trithorax homolog 2,Trx2,Wbp7,WBP-7,WW domain-binding protein 7
EIAAB40632 Histone-lysine N-methyltransferase SUV420H1,Rat,Rattus norvegicus,Su(var)4-20 homolog 1,Suppressor of variegation 4-20 homolog 1,Suv420h1,Suv4-20h1
EIAAB40637 Histone-lysine N-methyltransferase SUV420H2,Mouse,Mus musculus,Su(var)4-20 homolog 2,Suppressor of variegation 4-20 homolog 2,Suv420h2,Suv4-20h2
EIAAB40636 Histone-lysine N-methyltransferase SUV420H2,Rat,Rattus norvegicus,Su(var)4-20 homolog 2,Suppressor of variegation 4-20 homolog 2,Suv420h2,Suv4-20h2


 

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