Histone deacetylase

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* '''HDAC class I''' are homologous to yeast Rpd3.<br />
* '''HDAC class I''' are homologous to yeast Rpd3.<br />
* '''HDAC class II''' are homologous to yeast HdaI.<br />
* '''HDAC class II''' are homologous to yeast HdaI.<br />
-
* '''HDAC class III''' called '''sirtuin''' - (Silent Information Regulator) (SIRT) are NAD-dependent HDAC <ref>PMID:18249170</ref>.<br />
+
* '''HDAC class III''' called '''sirtuin''' - (Silent Information Regulator) (SIRT) are NAD-dependent HDAC. This protein is bifunctional and can act as a deacylase or as mono-ADP-acetyltransferase. <ref>PMID:18249170</ref>.<br />
For additional details see<br />
For additional details see<br />
* [[Understanding of the Recruitment of HDACs by MEF2, Based on Their Structure]]<br />
* [[Understanding of the Recruitment of HDACs by MEF2, Based on Their Structure]]<br />
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**[[4qa0]] - hHDAC8 (mutant) + SAHA<br />
**[[4qa0]] - hHDAC8 (mutant) + SAHA<br />
**[[5fcw]], [[5fue]] - hHDAC8 + hydroxamate<br />
**[[5fcw]], [[5fue]] - hHDAC8 + hydroxamate<br />
 +
**[[5vi6]] - hHDAC8 + trapoxin A<br />
**[[4qa1]], [[4qa2]], [[4qa3]], [[4qa4]] - hHDAC8 (mutant) + inhibitor<br />
**[[4qa1]], [[4qa2]], [[4qa3]], [[4qa4]] - hHDAC8 (mutant) + inhibitor<br />
**[[2v5w]] – hHDAC8 + tripeptide substrate<br />
**[[2v5w]] – hHDAC8 + tripeptide substrate<br />
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**[[2vqj]], [[2vqm]], [[4cbt]], [[5a2s]] – hHDAC4 catalytic domain + inhibitor<br />
**[[2vqj]], [[2vqm]], [[4cbt]], [[5a2s]] – hHDAC4 catalytic domain + inhibitor<br />
**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor
**[[2vqo]], [[2vqq]], [[2vqv]], [[4cby]] – hHDAC4 catalytic domain (mutant) + inhibitor
 +
 +
*HDAC5
 +
 +
**[[5uwi]] – hHDAC5 + RAN + RANBP1 + exportin<br />
*HDAC7
*HDAC7
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**[[3gv4]] - hHDAC6 zinc finger domain + ubiquitin peptide<br />
**[[3gv4]] - hHDAC6 zinc finger domain + ubiquitin peptide<br />
**[[3phd]] - hHDAC6 + polyubiquitin<br />
**[[3phd]] - hHDAC6 + polyubiquitin<br />
-
**[[5kh3]], [[5kh7]], [[5kh9]], [[5b8d]] – hHDAC6 zinc finger + inhibitor<br />
+
**[[5kh3]], [[5kh7]], [[5kh9]], [[5b8d]], [[6ce6]], [[6ce8]], [[6cea]], [[6cec]], [[6ced]], [[6cee]], [[6cef]], [[5wpb]], [[5wbn]] – hHDAC6 zinc finger + inhibitor<br />
 +
**[[5eem]] – zHDAC6 catalytic domain - zebrafish<br />
 +
**[[6cgp]], [[5wgm]], [[5wgl]], [[5wgi]], [[5wgk]], [[5g0j]], [[5g0i]], [[5g0h]], [[5g0g]], [[5g0f]], [[5efh]], [[5efg]], [[5efb]], [[5ef7]], [[5ef8]], [[5een]], [[5eek]], [[5eef]] – zHDAC6 catalytic domain + inhibitor <br />
 +
**[[5eei]] – zHDAC6 catalytic domain + SAHA<br />
 +
**[[5efn]], [[5efk]], [[53fj]] – zHDAC6 catalytic domain (mutant) + peptide <br />
 +
 
*'''HDAC class III'''
*'''HDAC class III'''
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**[[4l3o]], [[4y6l]], [[4y6o]] – hSIRT2 + acetyl lysine peptide + Zn<br />
**[[4l3o]], [[4y6l]], [[4y6o]] – hSIRT2 + acetyl lysine peptide + Zn<br />
**[[4x3o]], [[4x3p]] – hSIRT2 + myristoyl peptide + Zn<br />
**[[4x3o]], [[4x3p]] – hSIRT2 + myristoyl peptide + Zn<br />
-
**[[4rmg]], [[5dy4]], [[5dy5]] – hSIRT2 + inhibitor + Zn<br />
+
**[[4rmg]], [[5dy4]], [[5dy5]], [[5y5n]], [[5mat]] – hSIRT2 + inhibitor + Zn<br />
-
**[[5d7p]], [[5d7q]] – hSIRT2 + inhibitor + ADP-ribose + Zn<br />
+
**[[5d7p]], [[5d7q]], [[5mar]] – hSIRT2 + inhibitor + ADP-ribose + Zn<br />
**[[4rmh]], [[4rmi]] – hSIRT2 + acetyl lysine peptide + inhibitor + Zn<br />
**[[4rmh]], [[4rmi]] – hSIRT2 + acetyl lysine peptide + inhibitor + Zn<br />
**[[4r8m]] – hSIRT2 + peptide + tridecanethial + Zn<br />
**[[4r8m]] – hSIRT2 + peptide + tridecanethial + Zn<br />
**[[4rmj]] – hSIRT2 + ADP-ribose + nicotinamide + Zn <br />
**[[4rmj]] – hSIRT2 + ADP-ribose + nicotinamide + Zn <br />
 +
**[[5g4c]] – hSIRT2 + carba-NAD + Zn<br/ >
 +
**[[5fyq]] – hSIRT2 + RAN AA peptide + Zn<br/ >
 +
**[[5dy5]] – hSIRT2 + thiazole derivative + piperazine derivative + Zn<br/ >
 +
**[[5dy4]] – hSIRT2 + thiazole derivative + NAD + Zn<br/ >
 +
**[[5d7q]], [[5d7p]], [[5d7o]] – hSIRT2 + oxolan derivative + Zn<br/ >
*SIRT3
*SIRT3
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**[[5d7n]] – hSIRT3 + Zn<br />
**[[5d7n]] – hSIRT3 + Zn<br />
**[[3gls]] – hSIRT3 (mutant) + Zn<br />
**[[3gls]] – hSIRT3 (mutant) + Zn<br />
-
**[[3glu]] – hSIRT3 + peptide + Zn<br />
+
**[[3glu]], [[5ytk]], [[5y4h]] – hSIRT3 + peptide + Zn<br />
 +
**[[5bwo]], [[5bwn]] – hSIRT3 + palmitoyl H3K9 peptide + Zn<br />
 +
**[[5bwl]] – hSIRT3 + succinyl peptide + Zn<br />
**[[3glr]], [[3glt]], [[4fvt]], [[4bve]], [[4v1c]] – hSIRT3 + acetyl lysine peptide + Zn<br />
**[[3glr]], [[3glt]], [[4fvt]], [[4bve]], [[4v1c]] – hSIRT3 + acetyl lysine peptide + Zn<br />
**[[4hd8]] – hSIRT3 + acetyl lysine peptide + piceatannol + Zn<br />
**[[4hd8]] – hSIRT3 + acetyl lysine peptide + piceatannol + Zn<br />
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**[[4bvb]], [[4bvh]] – hSIRT3 + inhibitor + ADP-ribose + Zn<br />
**[[4bvb]], [[4bvh]] – hSIRT3 + inhibitor + ADP-ribose + Zn<br />
**[[4bvf]], [[4bvg]] – hSIRT3 + acetyl lysine peptide + inhibitor + Zn<br />
**[[4bvf]], [[4bvg]] – hSIRT3 + acetyl lysine peptide + inhibitor + Zn<br />
 +
**[[5h4d]] – hSIRT3 + agonist + NAD + Zn<br/ >
 +
 +
*SIRT4
 +
 +
**[[5ojn]] – hSIRT4 + ADP-ribose + Zn – ''Xenopus tropicalis''<br />
*SIRT5
*SIRT5
**[[2b4y]], [[4bn4]] – hSIRT5 + ADP-ribose + Zn<br />
**[[2b4y]], [[4bn4]] – hSIRT5 + ADP-ribose + Zn<br />
-
**[[2nyr]] – hSIRT5 + suramine + Zn<br />
+
**[[2nyr]], [[5xhs]] – hSIRT5 + inhibitor + Zn<br />
-
 
+
**[[3rig]], [[3riy]], [[4f4u]] – hSIRT5 + acetyl lysine peptide + Zn<br />
**[[3rig]], [[3riy]], [[4f4u]] – hSIRT5 + acetyl lysine peptide + Zn<br />
**[[4gic]] – hSIRT5 + acetyl lysine peptide + carba-NAD + Zn<br/ >
**[[4gic]] – hSIRT5 + acetyl lysine peptide + carba-NAD + Zn<br/ >
**[[4f56]] – hSIRT5 + peptide + intermediate + Zn<br />
**[[4f56]] – hSIRT5 + peptide + intermediate + Zn<br />
**[[4hda]] – hSIRT5 + acetyl lysine peptide + resveratrol + Zn<br />
**[[4hda]] – hSIRT5 + acetyl lysine peptide + resveratrol + Zn<br />
-
**[[4utn]], [[4utr]], [[4utv]], [[4utx]], [[4utz]], [[4uu7]], [[4uu8]], [[4uua]], [[4uub]] – zeSIRT5 + acetyl lysine peptide + inhibitor + Zn - zebrafish<br />
+
**[[4utn]], [[4utr]], [[4utv]], [[4utx]], [[4utz]], [[4uu7]], [[4uu8]], [[4uua]], [[4uub]], [[6flg]], [[6fkz]], [[6fky]] – zSIRT5 + acetyl lysine peptide + inhibitor + Zn <br />
-
 
+
**[[6enx]], [[6eo0]], [[6eqs]] – zSIRT5 + inhibitor + Zn <br />
 +
**[[5ojo]] – zSIRT5 + CPS1 peptide + Zn <br />
*SIRT6
*SIRT6
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**[[3pki]], [[3pkj]] – hSIRT6 (mutant) + ADP-ribose derivative + Zn<br />
**[[3pki]], [[3pkj]] – hSIRT6 (mutant) + ADP-ribose derivative + Zn<br />
**[[3zg6]] – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn<br />
**[[3zg6]] – hSIRT6 + acetyl lysine peptide + ADP-ribose + Zn<br />
 +
**[[5mgn]], [[5mfz]], [[5mfp]], [[5mf6]] – hSIRT6 + activator + Zn<br />
 +
 +
*SIRT7
 +
 +
**[[5iqz]] – hSIRT7 N-terminal<br />
}}
}}

Revision as of 05:58, 17 July 2018

Human sirtuin-3 complex with peptide containing acetylated lysine, sulfate, carbonate, glycerol and Zn+2 ion (PDB entry 3glr)

Drag the structure with the mouse to rotate

3D Structures of histone deacetylase

Updated on 17-July-2018


References

  1. ↑ Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, Nesvizhskii AI, Cristea IM. The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol. 2013;9:672. doi: 10.1038/msb.2013.26. PMID:23752268 doi:http://dx.doi.org/10.1038/msb.2013.26
  2. ↑ Schwer B, Verdin E. Conserved metabolic regulatory functions of sirtuins. Cell Metab. 2008 Feb;7(2):104-12. doi: 10.1016/j.cmet.2007.11.006. PMID:18249170 doi:http://dx.doi.org/10.1016/j.cmet.2007.11.006
  3. ↑ Marks P, Rifkind RA, Richon VM, Breslow R, Miller T, Kelly WK. Histone deacetylases and cancer: causes and therapies. Nat Rev Cancer. 2001 Dec;1(3):194-202. PMID:11902574 doi:http://dx.doi.org/10.1038/35106079
  4. ↑ Yamamoto H, Schoonjans K, Auwerx J. Sirtuin functions in health and disease. Mol Endocrinol. 2007 Aug;21(8):1745-55. Epub 2007 Apr 24. PMID:17456799 doi:http://dx.doi.org/10.1210/me.2007-0079
  5. ↑ Mann BS, Johnson JR, Cohen MH, Justice R, Pazdur R. FDA approval summary: vorinostat for treatment of advanced primary cutaneous T-cell lymphoma. Oncologist. 2007 Oct;12(10):1247-52. PMID:17962618 doi:http://dx.doi.org/10.1634/theoncologist.12-10-1247
  6. ↑ Jin L, Wei W, Jiang Y, Peng H, Cai J, Mao C, Dai H, Choy W, Bemis JE, Jirousek MR, Milne JC, Westphal CH, Perni RB. Crystal structures of human SIRT3 displaying substrate-induced conformational changes. J Biol Chem. 2009 Sep 4;284(36):24394-405. Epub 2009 Jun 16. PMID:19535340 doi:10.1074/jbc.M109.014928

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Michal Harel, Alexander Berchansky, Joel L. Sussman

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