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Histone methyltransferase: Difference between revisions

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<StructureSection load='1o9s' size='350' side='right' caption='Human histone-lysine N-methyltrasferase (magenta) complex with methylated lysine histone H3 peptide (green) and S-adenosyl homocysteine (SAH) (PDB entry [[1o9s]])' scene='46/467278/Cv/1'>
<StructureSection load='' size='350' side='right' caption='Human histone-lysine N-methyltrasferase (magenta) complex with methylated lysine histone H3 peptide (green) and S-adenosyl homocysteine (SAH) (PDB entry [[1o9s]])' scene='46/467278/Cv/1'>


== 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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== Structural highlights ==
== Structural highlights ==
Human <scene name='46/467278/Cv/5'>KHMT binds SAH in the peptide binding groove with the histone H3 peptide assuming an extended conformation and the methylated lysine</scene> inserted in a hydrophobic environment<ref>PMID:12540855</ref>. Water molecules shown as red spheres
Human <scene name='46/467278/Cv/6'>KHMT binds SAH in the peptide binding groove with the histone H3 peptide assuming an extended conformation and the methylated lysine</scene> inserted in a hydrophobic environment<ref>PMID:12540855</ref>. Water molecules shown as red spheres
</StructureSection>


== 3D Structures of histone methyltransferase ==
== 3D Structures of histone methyltransferase ==  
[[Histone methyltransferase 3D structures]]


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
</StructureSection>
{{#tree:id=OrganizedByTopic|openlevels=0|
 
*DOT1L histone methyltransferase
 
**[[1nw3]] – hHMT DOT1L – human
 
*Euchromatic histone methyltransferase
 
**[[2igq]] – hHMT-1 C terminal
 
*Histone-lysine N-methyltransferase
 
**[[2j8a]] – KHMT SET1 RRM domain – yeast
 
**[[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 />
**[[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 />
**[[4gnd]] - hKHMT Nsd3 Phd5-C5HCH<br />
**[[4rxj]] - hKHMT Nsd3 residues 953-1064<br />
**[[4yz8]], [[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 />
**[[1ml9]] – NcKHMT Dim-5 – ''Neurospora crassa''<br />
**[[1n3j]] – PvKHMT – Paramecium bursaria chlorella virus<br />
**[[1u2z]] – yKHMT C terminal<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 />
**[[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]] - hKHMT SETDB1 tudor domain + inhibitor<br />
**[[3sr4]], [[3uwp]], [[4ek9]], [[4ekg]], [[4eki]], [[4eqz]], [[4er0]], [[4er3]], [[4er5]], [[4er6]], [[4er7]], [[4hra]] - hKHMT catalytic domain + inhibitor<br />
**[[4wuy]] - hKHMT Smyd2 + inhibitor<br />
**[[5cpr]] - hKHMT Suv420 SET domain + 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 />
**[[3b95]] - hKHMT ankyrin repeat domain + H3 peptide<br />
**[[3lqi]], [[3lqj]] - hKHMT Mll1 3rd Phd finger and bromodomain + H3 peptide<br />
**[[5ex3]], [[5ex0]] - hKHMT Smyd3 + peptide<br />
**[[4l58]] - hKHMT PHD-type zinc finger domain + H3 peptide<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 />
 
*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 />
**[[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 />
**[[5hq8]] – hKHMT Smyd3 + SAH + MEKK2 peptide<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
 
**[[4e47]], [[4jds]], [[4jlg]], [[5ayf]] - hKHMT SET7/9 SET domain + SAM + inhibitor<br />
**[[3fpd]], [[3k5k]], [[3mo0]], [[3mo2]], [[3mo5]], [[3rjw]], [[4nvq]] - hKHMT SET domain + SAH + inhibitor<br />
**[[5tuz]] - hKHMT EHMT1 SET domain + SAH + inhibitor<br />
**[[5ttg]] - hKHMT EHMT1 catalytic domain + SAM + inhibitor<br />
**[[5tuy]] - 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]] – 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 />
**[[5t0m]], [[5t0k]] - hKHMT EHMT2 SET domain + SAM + SAH + H3 peptide<br />
**[[5ls6]], [[5hyn]] - hKHMT Ezh2 + polycomb protein + Jarid2 + inhibitor<br />
 
*Histone-arginine N-methyltransferase (Carm1)
 
**[[2v74]], [[2v7e]] – mRHMT catalytic domain <br />
**[[4c03]], [[4c06]], [[4c07]], [[4c08]], [[5hzm]] – mRHMT  6<br />
**[[2obq]] – rRHMT N terminal - rat <br />
**[[3b3g]], [[3b3j]] – rRHMT catalytic domain <br />
**[[4qqk]] – hRHMT 6 <br />
**[[4hc4]] – hRHMT 6 (mutant)<br />
 
*Histone-arginine N-methyltransferase (Carm1) binary complex
 
**[[5ih3]] – mRHMT  4 + SAH<br />
**[[5k8v]], [[5isi]], [[5ish]], [[5isg]], [[5isf]], [[5ise]], [[5isd]], [[5isc]], [[5isb]], [[5isa]], [[5is9]], [[5is8]], [[5is7]], [[5is6]] – mRHMT  4 + inhibitor<br />
**[[5lgs]], [[5lgr]], [[5lgq]], [[5lgp]] – mRHMT  4 + poly(A)-binding protein peptide + inhibitor<br />
**[[4c04]] – mRHMT  6 + inhibitor<br />
**[[4c05]], [[5fqo]], [[5fqn]] – mRHMT  6 + SAH<br />
**[[4c4a]] – mRHMT  7 + SAH<br />
**[[3b3f]] – rRHMT catalytic domain + SAH<br />
**[[5u4x]] – hRHMT 1 catalytic domain + SAH<br />
**[[5dxj]] – hRHMT 4 catalytic domain + sinefungin <br />
**[[4ikp]] – hRHMT 4 catalytic domain + purine derivative<br />
**[[5egs]] – hRHMT 6 + inhibitor<br />
 
*Histone-arginine N-methyltransferase (Carm1) ternary complex
 
**[[5lgs]], [[5lgr]], [[5lgq]], [[5lgp]] – mRHMT  4 + poly(A)-binding protein peptide + inhibitor<br />
**[[5dxa]], [[5dx8]], [[5dx1]] – hRHMT 4 catalytic domain + sinefungin + peptide<br />
**[[5dx0]], [[5dwq]] – hRHMT 4 catalytic domain + sinefungin + H3 peptide<br />
**[[2y1w]], [[2y1x]] – hRHMT 4 catalytic domain + sinefungin + indole inhibitor<br />
**[[4gqb]], [[5fa5]] – hRHMT 5 + methylsome protein 50 + H4 peptide<br />
**[[5emm]] – hRHMT 5 + methylsome protein 50 + sinefungin<br />
**[[5eml]] – hRHMT 5 + methylsome protein 50 + SAM<br />
**[[5emk]], [[5emj]], [[5c9z]] – hRHMT 5 + methylsome protein 50 + sinefungin + inhibitor<br />
**[[4x63]], [[4x61]], [[4x60]] – hRHMT 5 + methylsome protein 50 + SAH + inhibitor<br />
**[[5e8r]], [[4y30]], [[4y2h]] – hRHMT 6 + SAH + inhibitor<br />
**[[4qpp]] – hRHMT 6 (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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