Histone methyltransferase: Difference between revisions

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**[[2mdi]] - hKHMT SETD2 WW domain (mutant) - NMR<br />
**[[2mdi]] - hKHMT SETD2 WW domain (mutant) - NMR<br />
**[[5kh6]] - hKHMT SETDB1 tudor domain <br />
**[[5kh6]] - hKHMT SETDB1 tudor domain <br />
**[[5tfp]] - hKHMT SETDB2 N-terminal <br />
**[[2r3a]] – hKHMT Suv39H2<br />
**[[2r3a]] – hKHMT Suv39H2<br />
**[[3rq4]] - hKHMT Suv420H2<br />
**[[3rq4]] - hKHMT Suv420H2<br />
Line 61: Line 62:
**[[4mi0]] – hKHMT Ezh2<br />
**[[4mi0]] – hKHMT Ezh2<br />
**[[4mi5]] – hKHMT Ezh2 SET domain<br />
**[[4mi5]] – hKHMT Ezh2 SET domain<br />
**[[6by9]] - hKHMT EHMT1 residues 672-999<br />
**[[5v2n]] - hKHMT KMT5A residues 231-393<br />
**[[1ml9]] – NcKHMT Dim-5 – ''Neurospora crassa''<br />
**[[1ml9]] – NcKHMT Dim-5 – ''Neurospora crassa''<br />
**[[1n3j]] – PvKHMT – Paramecium bursaria chlorella virus<br />
**[[1n3j]] – PvKHMT – Paramecium bursaria chlorella virus<br />
Line 73: Line 76:
**[[4pzi]] – hKHMT CxxC domain + DNA <br />
**[[4pzi]] – hKHMT CxxC domain + DNA <br />
**[[3q0b]], [[3q0c]], [[3q0d]], [[3q0f]] – hKHMT SRA 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 />
**[[5ei9]], [[5eh2]], [[5egb]] - hKHMT Prdm9 zinc finger domain + DNA<br />
**[[4ygi]] – AtKHMT Suvh4 + DNA<br />
**[[4ygi]] – AtKHMT Suvh4 + DNA<br />
Line 99: Line 103:
**[[5th7]] – hKHMT SETD8 + inhibitor <br />
**[[5th7]] – hKHMT SETD8 + inhibitor <br />
**[[5t5g]] – hKHMT SETD8 (mutant) + inhibitor <br />
**[[5t5g]] – hKHMT SETD8 (mutant) + inhibitor <br />
**[[5ke3]], [[5ke2]], [[5kco]], [[5kch]] - hKHMT SETDB1 tudor domain + 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 />
**[[3sr4]], [[3uwp]], [[4ek9]], [[4ekg]], [[4eki]], [[4eqz]], [[4er0]], [[4er3]], [[4er5]], [[4er6]], [[4er7]], [[4hra]] - hKHMT catalytic domain + inhibitor<br />
**[[4wuy]] - hKHMT Smyd2 + inhibitor<br />
**[[4wuy]], [[6cby]], [[6cbx]], [[5wcg]] - hKHMT Smyd2 + inhibitor<br />
**[[5cpr]] - hKHMT Suv420 SET domain + inhibitor<br />
**[[5cpr]] - hKHMT Suv420 SET domain + inhibitor<br />
**[[5w1y]] - 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 />


*Histone-lysine N-methyltransferase binary complexes with polypeptide
*Histone-lysine N-methyltransferase binary complexes with polypeptide
Line 109: Line 117:
**[[3sw9]], [[3swc]] – hKHMT SET domain + peptide<br />
**[[3sw9]], [[3swc]] – hKHMT SET domain + peptide<br />
**[[4gne]], [[4gnf]], [[4gng]] - hKHMT Nsd3 Phd5-C5HCH + H3 peptide<br />
**[[4gne]], [[4gnf]], [[4gng]] - hKHMT Nsd3 Phd5-C5HCH + H3 peptide<br />
**[[6cen]] - hKHMT Nsd3 + inhibitor peptide<br />
**[[3b95]] - hKHMT ankyrin repeat domain + H3 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 />
**[[3lqi]], [[3lqj]] - hKHMT Mll1 3rd Phd finger and bromodomain + H3 peptide<br />
**[[5ex3]], [[5ex0]] - hKHMT Smyd3 + peptide<br />
**[[5ex3]], [[5ex0]] - hKHMT Smyd3 + peptide<br />
**[[5yvx]] - hKHMT Ashh2 CW domain + H3 peptide<br />
**[[4l58]] - hKHMT PHD-type zinc finger domain + H3 peptide<br />
**[[4l58]] - hKHMT PHD-type zinc finger domain + H3 peptide<br />
**[[6cko]] - zKHMT + AF-10 - zebrafish<br />


*Histone-lysine N-methyltransferase other binary complexes
*Histone-lysine N-methyltransferase other binary complexes
Line 142: Line 154:
**[[3s7d]], [[3s7f]], [[3tg5]] - hKHMT Smyd2 + SAH + p53 peptide<br />
**[[3s7d]], [[3s7f]], [[3tg5]] - hKHMT Smyd2 + SAH + p53 peptide<br />
**[[4o6f]] – hKHMT Smyd2 (mutant) + SAH + estrogen receptor 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 />
**[[5hq8]] – hKHMT Smyd3 + SAH + MEKK2 peptide<br />
**[[1zkk]] - hKHMT + SAH + H4 peptide <br />
**[[1zkk]] - hKHMT + SAH + H4 peptide <br />
Line 155: Line 169:


**[[4e47]], [[4jds]], [[4jlg]], [[5ayf]] - hKHMT SET7/9 SET domain + SAM + inhibitor<br />
**[[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 />
**[[3fpd]], [[3k5k]], [[3mo0]], [[3mo2]], [[3mo5]], [[3rjw]], [[4nvq]] - hKHMT SET domain + SAH + inhibitor<br />
**[[5tuz]] - hKHMT EHMT1 SET domain + SAH + inhibitor<br />
**[[5tuz]] - hKHMT EHMT1 SET domain + SAH + inhibitor<br />
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**[[5t0m]], [[5t0k]] - hKHMT EHMT2 SET domain + SAM + SAH + H3 peptide<br />
**[[5t0m]], [[5t0k]] - hKHMT EHMT2 SET domain + SAM + SAH + H3 peptide<br />
**[[5ls6]], [[5hyn]] - hKHMT Ezh2 + polycomb protein + Jarid2 + inhibitor<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)
*Histone-arginine N-methyltransferase (Carm1)
Line 183: Line 199:


**[[5ih3]] – mRHMT  4 + SAH<br />
**[[5ih3]] – mRHMT  4 + SAH<br />
**[[5k8v]], [[5isi]], [[5ish]], [[5isg]], [[5isf]], [[5ise]], [[5isd]], [[5isc]], [[5isb]], [[5isa]], [[5is9]], [[5is8]], [[5is7]], [[5is6]] – mRHMT  4 + inhibitor<br />
**[[5k8v]], [[5isi]], [[5ish]], [[5isg]], [[5isf]], [[5ise]], [[5isd]], [[5isc]], [[5isb]], [[5isa]], [[5is9]], [[5is8]], [[5is7]], [[5is6]], [[5tbj]], [[5tbi]], [[5tbh]], [[5ntc]], [[5lkj]], [[5k8x]], [[5k8w]] – mRHMT  4 + inhibitor<br />
**[[5lgs]], [[5lgr]], [[5lgq]], [[5lgp]] – mRHMT  4 + poly(A)-binding protein peptide + inhibitor<br />
**[[5lgs]], [[5lgr]], [[5lgq]], [[5lgp]] – mRHMT  4 + poly(A)-binding protein peptide + inhibitor<br />
**[[4c04]] – mRHMT  6 + inhibitor<br />
**[[4c04]] – mRHMT  6 + inhibitor<br />
Line 191: Line 207:
**[[5u4x]] – hRHMT 1 catalytic domain + SAH<br />
**[[5u4x]] – hRHMT 1 catalytic domain + SAH<br />
**[[5dxj]] – hRHMT 4 catalytic domain + sinefungin <br />
**[[5dxj]] – hRHMT 4 catalytic domain + sinefungin <br />
**[[4ikp]] – hRHMT 4 catalytic domain + purine derivative<br />
**[[4ikp]], [[6d2l]] – hRHMT 4 catalytic domain + purine derivative<br />
**[[5egs]] – hRHMT 6 + inhibitor<br />
**[[5egs]], [[5wcf]], [[5lv5]], [[5lv4]], [[5lv3]], [[5lv2]] – hRHMT 6 + inhibitor<br />


*Histone-arginine N-methyltransferase (Carm1) ternary complex
*Histone-arginine N-methyltransferase (Carm1) ternary complex
Line 200: Line 216:
**[[5dx0]], [[5dwq]] – hRHMT 4 catalytic domain + sinefungin + H3 peptide<br />
**[[5dx0]], [[5dwq]] – hRHMT 4 catalytic domain + sinefungin + H3 peptide<br />
**[[2y1w]], [[2y1x]] – hRHMT 4 catalytic domain + sinefungin + indole inhibitor<br />
**[[2y1w]], [[2y1x]] – hRHMT 4 catalytic domain + sinefungin + indole inhibitor<br />
**[[4gqb]], [[5fa5]] – hRHMT 5 + methylsome protein 50 + H4 peptide<br />
**[[6arv]], [[6arj]] – hRHMT 4 catalytic domain + SAH +  inhibitor<br />
**[[5emm]] – hRHMT 5 + methylsome protein 50 + sinefungin<br />
**[[4gqb]], [[5fa5]] – hRHMT 5 + methylosome protein 50 + H4 peptide<br />
**[[5eml]] – hRHMT 5 + methylsome protein 50 + SAM<br />
**[[5emm]] – hRHMT 5 + methylosome protein 50 + sinefungin<br />
**[[5emk]], [[5emj]], [[5c9z]] – hRHMT 5 + methylsome protein 50 + sinefungin + inhibitor<br />
**[[5eml]] – hRHMT 5 + methylosome protein 50 + SAM<br />
**[[4x63]], [[4x61]], [[4x60]] – hRHMT 5 + methylsome protein 50 + SAH + inhibitor<br />
**[[5emk]], [[5emj]], [[5c9z]] – hRHMT 5 + methylosome protein 50 + sinefungin + inhibitor<br />
**[[4x63]], [[4x61]], [[4x60]] – hRHMT 5 + methylosome protein 50 + SAH + inhibitor<br />
**[[6ckc]] – hRHMT 5 + methylsome protein 50 + inhibitor<br />
**[[5e8r]], [[4y30]], [[4y2h]] – hRHMT 6 + SAH + inhibitor<br />
**[[5e8r]], [[4y30]], [[4y2h]] – hRHMT 6 + SAH + inhibitor<br />
**[[4qpp]] – hRHMT 6 (mutant) + peptide + inhibitor<br />
**[[4qpp]] – hRHMT 6 (mutant) + peptide + inhibitor<br />

Revision as of 13:37, 17 July 2018


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[1]. 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.

Relevance

Inhibitors of the histone-lysine N-methyltransferase SMYD2 which represses the tumor-suppressing activities of p53 are studied as cancer therapy drugs[2].

Disease

Aberrant HMT plays a role in cancer, intellectual disability syndromes and regulation of tissue aging[3].

Structural highlights

Human inserted in a hydrophobic environment[4]. Water molecules shown as red spheres

Human histone-lysine N-methyltrasferase (magenta) complex with methylated lysine histone H3 peptide (green) and S-adenosyl homocysteine (SAH) (PDB entry 1o9s)

Drag the structure with the mouse to rotate

3D Structures of histone methyltransferase3D Structures of histone methyltransferase

Updated on 17-July-2018

ReferencesReferences

  1. ↑ Trievel RC. Structure and function of histone methyltransferases. Crit Rev Eukaryot Gene Expr. 2004;14(3):147-69. PMID:15248813
  2. ↑ Ferguson AD, Larsen NA, Howard T, Pollard H, Green I, Grande C, Cheung T, Garcia-Arenas R, Cowen S, Wu J, Godin R, Chen H, Keen N. Structural Basis of Substrate Methylation and Inhibition of SMYD2. Structure. 2011 Jul 20. PMID:21782458 doi:10.1016/j.str.2011.06.011
  3. ↑ Greer EL, Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet. 2012 Apr 3;13(5):343-57. doi: 10.1038/nrg3173. PMID:22473383 doi:http://dx.doi.org/10.1038/nrg3173
  4. ↑ Xiao B, Jing C, Wilson JR, Walker PA, Vasisht N, Kelly G, Howell S, Taylor IA, Blackburn GM, Gamblin SJ. Structure and catalytic mechanism of the human histone methyltransferase SET7/9. Nature. 2003 Feb 6;421(6923):652-6. Epub 2003 Jan 22. PMID:12540855 doi:10.1038/nature01378

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Michal Harel, Alexander Berchansky, Joel L. Sussman
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