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Histone methyltransferase: Difference between revisions

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== Function ==
== Function ==
'''Histone methyltransferase''' (HMT) are '''histone-lysine N-methyltransferase''' (KHMT)  and '''histone-arginine N-methyltransferase''' (RHMT)  which catalyzes the transfer of methyl groups to lysine and arginine residues of histones<ref>PMID:15248813</ref>.  HMT use S-adenosyl methionine (SAM) or S-adenosyl homocysteine (SAH) as the methyl donor.  KHMT can be SET domain-containing or non-SET domain-containing.  The SET domain contains the catalytic core of KHMT and targets the lysine tail region of KHMT.  CxxC domain is a zinc finger domain.
'''Histone methyltransferase''' (HMT) are '''histone-lysine N-methyltransferase''' (KHMT)  and '''histone-arginine N-methyltransferase''' (RHMT)  which catalyzes the transfer of methyl groups to lysine and arginine residues of histones<ref>PMID:15248813</ref>.  HMT use S-adenosyl methionine (SAM) or S-adenosyl homocysteine (SAH) as the methyl donor.  KHMT can be SET domain-containing or non-SET domain-containing.  The SET domain contains the catalytic core of KHMT and targets the lysine tail region of KHMT.  CxxC domain is a zinc finger domain.
For SET7/9 see [[Histone Lysine Methyltransferase SET7/9]].
*'''euchromatin histone methyltransferase''' dimethylates histone H3 at Lys 9 resulting in transcriptional repression<ref>PMID:32684241</ref>.
*'''DOT1L histone methyltransferase''' methylates histone H3 at Lys 79 resulting in transcriptional repression<ref>PMID:35495127</ref>.


== Relevance ==
== Relevance ==
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</StructureSection>
</StructureSection>


== 3D Structures of histone methyltransferase == 
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|
*DOT1L histone methyltransferase
**[[1nw3]] – hHMT DOT1L – human
*Euchromatic histone methyltransferase
**[[2igq]] – hHMT-1 C terminal
*Histone-lysine N-methyltransferase
**[[3s8s]] – hKHMT SETD1A RRM domain<br />
**[[2mdc]], [[2mdj]] - hKHMT SETD2 WW domain - NMR<br />
**[[2mdi]] - hKHMT SETD2 WW domain (mutant) - NMR<br />
**[[5kh6]] - hKHMT SETDB1 tudor domain <br />
**[[5tfp]] - hKHMT SETDB2 N-terminal <br />
**[[2r3a]] – hKHMT Suv39H2<br />
**[[3rq4]] - hKHMT Suv420H2<br />
**[[3s8p]] - hKHMT Suv420H1<br />
**[[3mts]] - hKHMT Suv39H1 chromo domain<br />
**[[1h3i]] - hKHMT SET7/9 residues 52-344<br />
**[[2o8j]] - hKHMT H3K9 residues 913-1193<br />
**[[5f5e]] – Mll1 residues 3813-3969<br />
**[[5f59]] – Mll3 residues 4757-4910<br />
**[[2lv9]] - hKHMT Mll5 residues 109-188 - NMR<br />
**[[5ht6]] - Mll5 residues 323-458<br />
**[[2kyu]] - hKHMT Mll Phd3 finger – NMR<br />
**[[6g3t]], [[6g3p]] - hKHMT Nsd3 residues 247-398<br />
**[[4gnd]] - hKHMT Nsd3 Phd5-C5HCH 1310-1413<br />
**[[4rxj]] - hKHMT Nsd3 residues 953-1064<br />
**[[5upd]]- hKHMT Nsd3 residues 1054-1285<br />
**[[3lqh]] - hKHMT Mll Phd bromodomain<br />
**[[3b7b]] - hKHMT ankyrin repeat domains 2-7<br />
**[[3bo5]] – hKHMT Setmar methyltransferase domain <br />
**[[3k9j]], [[3k9k]] – hKHMT Setmar transposable domain (mutant)<br />
**[[3dlm]] - hKHMT Setmdb1 Tudor domain <br />
**[[3n71]] - hKHMT Smyd1<br />
**[[5hi7]] - hKHMT Smyd3<br />
**[[3rsn]], [[3s32]] – hKHMT Ash2 N terminal<br />
**[[3toj]] – hKHMT Ash2 Spry domain<br />
**[[4ijd]] – hKHMT Prdm9<br />
**[[4mi0]] – hKHMT Ezh2<br />
**[[4mi5]] – hKHMT Ezh2 SET domain<br />
**[[6by9]] - hKHMT EHMT1 residues 672-999<br />
**[[5v2n]] - hKHMT KMT5A residues 231-393<br />
**[[2j8a]] – KHMT SET1 RRM domain – yeast<br />
**[[1u2z]] – yKHMT C terminal<br />
**[[1ml9]] – NcKHMT Dim-5 – ''Neurospora crassa''<br />
**[[1n3j]] – PvKHMT – Paramecium bursaria chlorella virus<br />
**[[2l7p]] – AtKHMT Ashh2 CW domain – ''Arabidopsis thaliana'' - NMR<br />
**[[2lxe]] – AtKHMT Suvr4 SET31 - NMR<br />
*Histone-lysine N-methyltransferase binary complexes with DNA
**[[2kkf]] – hKHMT Hrx CxxC domain + DNA – NMR<br />
**[[4nw3]] – hKHMT Mll CxxC domain + DNA <br />
**[[4pzi]] – hKHMT CxxC domain + DNA <br />
**[[3q0b]], [[3q0c]], [[3q0d]], [[3q0f]] – hKHMT SRA domain + DNA <br />
**[[5vc8]] - hKHMT Nsd2 + DNA<br />
**[[5ei9]], [[5eh2]], [[5egb]] - hKHMT Prdm9 zinc finger domain + DNA<br />
**[[4ygi]] – AtKHMT Suvh4 + DNA<br />
*Histone-lysine N-methyltransferase binary complexes with methyl donor
**[[4z4p]] – hKHMT Mll4 SET domain + SAH <br />
**[[3qow]] – hKHMT + SAM <br />
**[[4ynm]] – hKHMT Ash1L + SAM <br />
**[[4ypu]], [[4ype]], [[4ypa]], [[4ynp]] – hKHMT Ash1L (mutant) + SAM <br />
**[[4h12]], [[5jle]] – hKHMT SETD2 catalytic domain + SAH <br />
**[[3smt]] – hKHMT SETD3 + SAM <br />
**[[4bup]], [[3ooi]] – hKHMT SET domain + SAM <br />
**[[3qox]], [[3sx0]] – hKHMT + SAH <br />
**[[2w5y]] – hKHMT Hrx methyltransferase domain + SAH <br />
**[[3rib]] – hKHMT Smyd2 + SAH<br />
**[[3s7j]], [[3tg4]] - hKHMT Smyd2 + SAM<br />
**[[1mt6]] - hKHMT SET7/9 residues 58-337 + SAH<br />
**[[1n6a]] – hKHMT SET7/9 SET domain + SAM<br />
**[[1n6c]] – hKHMT SET7/9 residues 70-366 + SAM<br />
*Histone-lysine N-methyltransferase binary complexes with inhibitor
**[[5mw4]], [[5mw3]], [[5mvs]], [[5juw]], [[5dtr]], [[5dtq]], [[5dtm]], [[5dt2]], [[5dsx]], [[5dry]], [[5drt]], [[4wvl]] – hKHMT DOT1L + inhibitor <br />
**[[4fmu]], [[5lt8]], [[5lt7]], [[5lt6]], [[5lsz]], [[5lsy]], [[5lsx]], [[5lsu]], [[5lss]] – hKHMT SETD2 + inhibitor <br />
**[[5th7]] – hKHMT SETD8 + inhibitor <br />
**[[5t5g]] – hKHMT SETD8 (mutant) + inhibitor <br />
**[[5ke3]], [[5ke2]], [[5kco]], [[5kch]], [[6bpi]], [[6au3]], [[6au2]] - hKHMT SETDB1 tudor domain + inhibitor<br />
**[[3sr4]], [[3uwp]], [[4ek9]], [[4ekg]], [[4eki]], [[4eqz]], [[4er0]], [[4er3]], [[4er5]], [[4er6]], [[4er7]], [[4hra]] - hKHMT catalytic domain + inhibitor<br />
**[[4wuy]], [[6cby]], [[6cbx]], [[5wcg]] - hKHMT Smyd2 + inhibitor<br />
**[[5cpr]] - hKHMT Suv420 SET domain + inhibitor<br />
**[[6p0r]] - hKHMT Suv39h2 SET domain + inhibitor<br />
**[[5w1y]], [[6boz]] - hKHMT KMT5A SET domain (mutant) + inhibitor<br />
**[[5wbv]] - hKHMT KMT5B SET domain + inhibitor<br />
**[[5vsf]], [[5vsd]], [[5vpj]] - hKHMT EHMT1 SET domain + inhibitor<br />
**[[5vse]], [[5vsc]], [[5vpi]] - hKHMT EHMT2 SET domain + inhibitor<br />
**[[6nm4]] - hKHMT Prdm9 zinc finger domain + inhibitor<br />
**[[6g2o]], [[6g2f]], [[6g2e]], [[6g2c]], [[6g2b]], [[6g29]], [[6g27]], [[6g25]], [[6g24]] - hKHMT Nsd3 residues 247-398 + inhibitor<br />
*Histone-lysine N-methyltransferase binary complexes with polypeptide
**[[3f2k]] – hKHMT Setmar SET domain + LYFA peptide<br />
**[[3sw9]], [[3swc]] – hKHMT SET domain + peptide<br />
**[[4gne]], [[4gnf]], [[4gng]] - hKHMT Nsd3 Phd5-C5HCH + H3 peptide<br />
**[[6cen]] - hKHMT Nsd3 + inhibitor peptide<br />
**[[6mon]] - hKHMT Smyd2 + inhibitor peptide<br />
**[[3b95]] - hKHMT ankyrin repeat domain + H3 peptide<br />
**[[6bhi]], [[6bhh]], [[6bhg]], [[6bhe]], [[6bhd]] - hKHMT SETDB1 tudor domain + H3 peptide<br />
**[[3lqi]], [[3lqj]] - hKHMT Mll1 3rd Phd finger and bromodomain + H3 peptide<br />
**[[6mlc]] - hKHMT Mll3 Phd7 domain + H4 peptide <br />
**[[6o7g]] - hKHMT Mll4 Phd6 domain + H4 peptide - NMR<br />
**[[5ex3]], [[5ex0]] - hKHMT Smyd3 + peptide<br />
**[[5yvx]] - hKHMT Ashh2 CW domain + H3 peptide<br />
**[[6hbo]] - hKHMT Ashh2 CW domain + H3 peptide - NMR<br />
**[[4l58]] - hKHMT PHD-type zinc finger domain + H3 peptide<br />
**[[6cko]] - zKHMT + AF-10 - zebrafish<br />
*Histone-lysine N-methyltransferase other binary complexes
**[[3cbp]] - hKHMT SET7/9 SET domain + sinefungin<br />
**[[3vuz]], [[3vv0]] - hKHMT SET7/9 SET domain + deoxyadenosine derivative<br />
**[[4x8p]], [[4x8n]] – hKHMT Ash2L Spry domain + RBBP5 <br />
**[[6e2h]] – hKHMT SET/Ash2 + DPY-30L <br />
*Histone-lysine N-methyltransferase ternary complex containing polypeptide
**[[2w5z]] – hKHMT Hrx methyltransferase domain + SAH + histone peptide<br />
**[[5v22]], [[5v21]], [[5jlb]], [[5jjy]] - hKHMT SETD2 SET domain + SAH + H3 peptide<br />
**[[1o9s]] - hKHMT SET7/9 SET domain + SAH + H3 peptide<br />
**[[2bqz]] - hKHMT SET7 SET domain + SAH + H4 peptide<br />
**[[6mbl]], [[6mbk]], [[6mbj]], [[6icv]], [[6ict]] - hKHMT SETD3 + SAH + actin peptide<br />
**[[3f9w]], [[3f9x]], [[3f9y]], [[3f9z]] - hKHMT SETD8 SET domain + SAH + H4 peptide<br />
**[[5teg]] - hKHMT SETD8 SET domain + SAM + H4 peptide<br />
**[[5eg2]] - hKHMT SETD7 SET domain + SAH + TAF10 peptide<br />
**[[4ij8]] - hKHMT SETD8 + SAM + H3 peptide<br />
**[[4j7i]], [[4j83]], [[4j8o]], [[4j7f]] - hKHMT SETD7 + SAH + TFIID peptide<br />
**[[2rfi]], [[3hna]] - hKHMT H3K9 catalytic domain + SAH + H3 peptide<br />
**[[1xqh]] - hKHMT SET7/9 SET domain + SAH + p53 peptide<br />
**[[2f69]], [[3m53]] - hKHMT SET7/9 SZET domain + SAH + TAF10 peptide<br />
**[[3m54]], [[3m55]], [[3m56]], [[3m57]], [[3m58]], [[3m59]], [[3m5a]] - hKHMT SET7/9 SET domain (mutant) + SAH + TAF10 peptide<br />
**[[3cbm]] - hKHMT SET7/9 SET domain + SAM + estrogen receptor peptide<br />
**[[3cbo]] - hKHMT SET7/9 SET domain + SAH + estrogen receptor peptide<br />
**[[3os5]] - hKHMT SET7/9 SET domain + SAH + DNMT1 peptide<br />
**[[3qxy]], [[3rc0]] - hKHMT SETD6 SET domain + p65 peptide + SAM<br />
**[[5jj0]], [[5jiy]], [[5jin]], [[5jhn]] - hKHMT EHMT2 SET domain + SAM + H3 peptide<br />
**[[3s7d]], [[3s7f]], [[3tg5]] - hKHMT Smyd2 + SAH + p53 peptide<br />
**[[4o6f]] – hKHMT Smyd2 (mutant) + SAH + estrogen receptor peptide<br />
**[[5v3h]] – hKHMT Smyd2 (mutant) + SAM + inhibitor<br />
**[[5v37]] – hKHMT Smyd3 + SAM + inhibitor<br />
**[[5hq8]] – hKHMT Smyd3 + SAH + MEKK2 peptide<br />
**[[6ine]], [[6ago]] – hKHMT Ash1L + MRG15 + SAM <br />
**[[1zkk]] - hKHMT + SAH + H4 peptide <br />
**[[4c1q]] - hKHMT SET domain + SAH + H3 peptide <br />
**[[4i51]] - hKHMT (mutant) + SAH + H3 peptide <br />
**[[5f6l]] – hKHMT Mll1 (mutant) + RBBP5 + Ash2L<br />
**[[5f6k]] – hKHMT Mll3 + RBBP5 + Ash2L + peptide<br />
**[[1peg]] - NcKHMT Dim-5 + SAH + H3 peptide<br />
**[[2g46]] – PvKHMT + SAH + H3 peptide<br />
**[[4au7]] - mKHMT + SAH + H4 peptide - mouse<br />
*Histone-lysine N-methyltransferase ternary complex containing inhibitor; Domains – catalytic 879-1159; SET 1006-1266
**[[4e47]], [[4jds]], [[4jlg]], [[5ayf]] - hKHMT SET7/9 SET domain + SAM + inhibitor<br />
**[[5ylt]] - hKHMT SET7/9 SET domain + sinefungin + inhibitor<br />
**[[3fpd]], [[3k5k]], [[3mo0]], [[3mo2]], [[3mo5]], [[3rjw]], [[4nvq]] - hKHMT SET domain + SAH + inhibitor<br />
**[[5tuz]], [[6mbp]], [[6mbo]] - hKHMT EHMT1 SET domain + SAH + inhibitor<br />
**[[5ttg]], [[5v9j]] - hKHMT EHMT1 catalytic domain + SAM + inhibitor<br />
**[[5tuy]], [[5v9i]] - hKHMT EHMT2 SET domain + SAM + inhibitor<br />
**[[5ttf]] - hKHMT EHMT2 catalytic domain + SAM + inhibitor<br />
**[[3s7b]], [[5kjn]], [[5kjm]], [[5kjl]], [[5kjk]], [[5arg]], [[5arf]], [[4ynd]] - hKHMT Smyd2 + SAM + inhibitor<br />
**[[5ccm]], [[5ccl]], [[5yjo]], [[5xxj]], [[5xxg]], [[5xxd]] – hKHMT Smyd3 + SAM + inhibitor<br />
**[[1zkk]] - hKHMT + SAH + H4 peptide <br />
**[[4qen]], [[4qeo]], [[4qep]] – AtKHMT Suvh4 + DNA + SAH<br />
*Histone-lysine N-methyltransferase higher complexes
**[[5hq2]] - hKHMT SETD8 SET domain + H3 + H4 + H2 + SRM1 + DNA<br />
**[[6jm9]] - hKHMT DOT1 + H3.2 + H4 + H2A + H2B + DNA – Cryo EM<br />
**[[6o96]], [[6nqa]], [[6nog]], [[6nn6]], [[6nj9]], [[6jma]], [[6j99]] - hKHMT DOT1 + H3.2 + H4 + H2A + H2B + polyubiquitin + DNA – Cryo EM<br />
**[[5t0m]], [[5t0k]] - hKHMT EHMT2 SET domain + SAM + SAH + H3 peptide<br />
**[[5ls6]], [[5hyn]] - hKHMT Ezh2 + polycomb protein + Jarid2 + inhibitor<br />
**[[6c24]], [[6c23]] - hKHMT Ezh2 + polycomb repressor complex 2 – Cryo EM<br />
*Histone-arginine N-methyltransferase (Carm1)
**[[4qqk]] – hPRMT6 <br />
**[[4hc4]] – hPRMT6 (mutant)<br />
**[[2v74]], [[2v7e]] – mPRMT catalytic domain <br />
**[[4c03]], [[4c06]], [[4c07]], [[4c08]], [[5hzm]] – mPRMT6<br />
**[[2obq]] – rPRMT N terminal - rat <br />
**[[3b3g]], [[3b3j]] – rPRMT catalytic domain <br />
*Histone-arginine N-methyltransferase (Carm1) binary complex
**[[5u4x]] – hPRMT1 catalytic domain + SAH<br />
**[[6nt2]] – hPRMT1 residues 1-371 + inhibitor<br />
**[[5dxj]] – hPRMT4 catalytic domain + sinefungin <br />
**[[4ikp]], [[6d2l]], [[6dvr]] – hPRMT4 catalytic domain + purine derivative<br />
**[[5egs]], [[5wcf]], [[5lv5]], [[5lv4]], [[5lv3]], [[5lv2]] – hPRMT6 + inhibitor<br />
**[[5ih3]] – mPRMT4 + SAH<br />
**[[5k8v]], [[5isi]], [[5ish]], [[5isg]], [[5isf]], [[5ise]], [[5isd]], [[5isc]], [[5isb]], [[5isa]], [[5is9]], [[5is8]], [[5is7]], [[5is6]], [[5tbj]], [[5tbi]], [[5tbh]], [[5ntc]], [[5lkj]], [[5k8x]], [[5k8w]] – mPRMT4 + inhibitor<br />
**[[5lgs]], [[5lgr]], [[5lgq]], [[5lgp]] – mPRMT4 + poly(A)-binding protein peptide + inhibitor<br />
**[[4c04]] – mPRMT6 + inhibitor<br />
**[[4c05]], [[5fqo]], [[5fqn]] – mPRMT6 + SAH<br />
**[[4c4a]] – mPRMT7 + SAH<br />
**[[6ogn]] – mPRMT7 + inhibitor<br />
**[[3b3f]] – rPRMT catalytic domain + SAH<br />
*Histone-arginine N-methyltransferase (Carm1) ternary complex
**[[5dxa]], [[5dx8]], [[5dx1]] – hPRMT4 catalytic domain + sinefungin + peptide<br />
**[[5dx0]], [[5dwq]] – hPRMT4 catalytic domain + sinefungin + H3 peptide<br />
**[[2y1w]], [[2y1x]] – hPRMT4 catalytic domain + sinefungin + indole inhibitor<br />
**[[6arv]], [[6arj]] – hPRMT4 catalytic domain + SAH +  inhibitor<br />
**[[5lgs]], [[5lgr]], [[5lgq]], [[5lgp]] – mPRMT 4 + poly(A)-binding protein peptide + inhibitor<br />
**[[4gqb]], [[5fa5]] – hPRMT5 + methylosome protein 50 + H4 peptide<br />
**[[5emm]] – hPRMT5 + methylosome protein 50 + sinefungin<br />
**[[6k1s]] – hPRMT5 + methylosome protein 50 + inhibitor<br />
**[[5eml]] – hPRMT5 + methylosome protein 50 + SAM<br />
**[[5emk]], [[5emj]], [[5c9z]] – hPRMT5 + methylosome protein 50 + sinefungin + inhibitor<br />
**[[4x63]], [[4x61]], [[4x60]] – hPRMT5 + methylosome protein 50 + SAH + inhibitor<br />
**[[6ckc]] – hPRMT5 + methylosome protein 50 + inhibitor<br />
**[[5e8r]], [[4y30]], [[4y2h]], [[6p7i]] – hPRMT6 + SAH + inhibitor<br />
**[[4qpp]] – hPRMT6 (mutant) + peptide + inhibitor<br />
}}
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman
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